I think you can assume that they would expect SOME kind of defense, or at least try to find "it" regardless if there is any, simply because SOME labs most certainly will have defenses, and as there isnt any limit on what you can use for it, you damn well better be prepared even if 90% of magi doesnt have defenses, or you might end up a head shorter.
I agree that the SG is not the enemy but he is the one generating the stories. Playing fair or not he is the one to decide whether the story is someone stole your research or someone got caught stealing your research.
The real irony of the situation is that while if the players spend a ton of time defending their sancta then that quit possibly is a signal to the Story Guide that they want to deal with sanctum violators as a plot line. While the opposite almost always means that the players have no interest in such stories.
There is also the point that there would be legal difficulties if you invade another magi's sanctum with out some form of legal protection like Wizard War. If you took something it would be depriving a magus of their magic, by and large anyway. I believe there is the example of a magus breaking into anothers sactum to steal vis because the second magus was not repaying a debt, but other than things like that breaking in is a no no, and the quesators would like to have words with those who violate it.
Depends on the situation. If the SG wants a story that will have stuff stolen then stuff will get stolen somehow. If it is an existing enemy who is trying to hurt the magus by stealing their stuff then he might or might not get in.
We had a discussion about this and my Mercere Mutantum specialist had an idea of a Mu/Vi(ig) effect which converted any active spells in the room to be turned to fire. Despite the Ludicrously high level of this effect and the inherent dangers of setting ones own lab on fire, it was going to need a huge penetration to effect Hermetic interlopers. Needless to say this is still on his 'to do' list.
However spells to turn spells back upon interlopers (and the ability to turn these defences off) are doable, but need a bit more lateral thought.
A device with an environmental trigger which would go off if the door was opened UNLESS some codeword was said is doable with a plethora of linked effects including rego or perdo vim magic supression
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Right. The entire Code is based on the principle of retribution. All you are required to do is put a symbol that says "this is my sanctum". If it is violated, you don't have to only deal with the Magus, you have to deal with the Order. And the Order will collectively have the talent to hunt down damn near anyone and kill them, if the Order is sufficiently motivated. (if it can't, your petty defenses won't stop the intruder either).
In practice, most Sanctum locations are inside covenants that have basic physical security (walls, some guards, but not so many as to piss off the local lords, an Aegis that stops the dumb minor faerie or demon but does nothing to protect against a powerful one, or a magus who ignores the Code rules). The law doesn't require it, but common sense says "do the easy stuff, to keep those too stupid to know better out".
A lot of mages could put up day or month-wards, with spontaneous magic if nothing else. But it is drudgery to maintain such things for an event that will rarely if ever happen. (that kind of event is tailor made for rituals like Waiting spell/watching ward - a one time higher cost but you only have to refresh it if the problem you put it out there for actually happens)
It's those one time devices/traps/wards that you watch out for when going into a renounced magus's Sanctum. They could be of any power level and hugely destructive. But your average magus won't have anything there at all, or at worst a minor alarm-type spell in the kinds of campaigns described in the canon literature. (be a bit more cautious with Flambeau and especially Tytalus)
Yes and no. If a player has his magus pend a lot of time and vis to protect himself, his sanctum should be more difficult to plunder by enemies than those who don't. OTOH it could make for just as good a story if a magus returns home to find his sanctum half-way breached and some of his defences busted in the process.
It is also based on the idea of might makes right, it would be easy to take something from someone enough weaker than you to declare wizards war for expressly that purpose. Doing that often might be unwise, as no Magus can stand up to even a few magi who are willing to spend enough seasons working specifically to deal with the issue. Charged items seriously favor the attacker as a general rule.
Calling up a posse to make an unofficial march against someone is a long standing tradition as well.
You could make a magic item which is triggered by some environmental effect.
Was a brass toggle/panel in the door turned 180 degrees before the door was opened. Have this with some Intellego terram type effects and a linked trigger and if the door is opened (it moves in space) WITHOUT the toggle turned then this link triggers some effect such as a Diameter Duration poisonous gas with penetration up in the many of tens.
It could also trigger an alarm, seal the windows and walls of the sanctum in stone transport things in a certain area to another locations (Such as a cheast filled with Enchantments, vis and so on) being blinked to a more secure location.
I even considered a spell which was a Rego-Animal type spell to spontaneously fill a room with wasps.
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On this subject, do anyone have a nice way to detect invisible intruders?
Fill your lab with imaginem species and do a InIm to see through your own illusions (while knowing they are here, which can need +1 or more magnitude if the SG is reading the guideline straigthly or not).
The place where none is is the place where is a PeIm effect and an hermetic invisible person.
Do an automata with second sight? (i'm not familiar with them) and if he sees something, let him triggers a "kill all" effect in your lab? or a "send me a mental warning" so that you know that there is someone invisible in your lab wherever you are.
An item that detects active magics of 5th magnitude or above. Put a linked trigger to another spell and there you go. Only works if you are not in your sanctum, but besides that it is quite OK.
Also, at least one Confraternity requires you to invade a sanctum and steal an item as an initiation Quest. These guys probably get pretty inventive in protecting their sancta (sanctae? sanctums?).
Well, graduates of the AD&D Academy cover the floor in flour, in order to see their footsteps. Or cornflakes to hear invisible people sneaking around... 
Or else I'm thinking InIm, like the Quaesitorial spell The Discerning Eye from HoH:TL
The easiest way is to fill the room with something that will either stick to or have a 'hole' where the invisible person is. It doesn't matter if its creo-magic'd or not - a person with parma will make a parma-shaped hole in your cloud of whatever-it-is. Creo Auram would be the safest and simplest, and can probably be spont'd by almost any magus more than 5 years out of apprenticeship. The magnitude is probably low enough that you could make an item to do it as a side project while working on some more impressive Creo Auram device, or just buy one from a passing Redcap for ~3-4 pawns.
I don't know about invisible intruders , but for intruders with Second Sight or See the Unvisionable spells ,
a thick , room-blanketing invisible to normal sight fog.
Make sure it has penetration higher than anything else in the room , if possible.
That way , they will not be able to target anything otherwise invisible in your sanctum.
If they are using scent-based targeting , make your invisible fog rose-scented (or worse).
Have a door, and something or someone that watches the door, and yells if it opens without cause.
Seriously, doors have foiled more invisible PC's than any other defence I've seen in over 30 years of gaming.
The other suggestions are good too.