Advantages.
It's much harder to steal a boat than an enchanted item.
You can't "sink" the boat by throwing the item out of the porthole
Range self rather than range touch saves a magnitude on all of the effects that target the boat
Oh my. It's a Holo-deck!
Not necessarily.
It's easier to put an item into your pocket than a boat under your cloak, but it's far more likely for pirates or brigands (or a powerful mundane lord) to target a boat, esp one reputed to fly, than for them to know where a small item is being kept, or even be aware of the existence and details of that item in the first place to know to try.
(If I were the mage with the item, I'd keep it somewhere very safe. If I had the boat, then most likely, I'd keep it... at a dock, or be limited to wherever it would fit.)
As I said above, this aspect is "arguable".
The +1 magnitude effect is a good point.
re Acts of Gross Stupity- see security, above. (And I'd bet it could be easily found with magic if it went overboard.)
I'm just saying that when the villianous non-hermetic shapeshifter changes into an African swallow and flys out of ship carrying your item when you're crusing at 400 meters you'll breifly wish that you'd enchanted the ship rather than the item. (insert discussion about dispelling constant duration effects here)
Actually, I agree with your points, you asked for advantages I and I tried to come up with some.
(double post)
Yeah, and thanks for that. I guess for me, anything desirable can be stolen. So it comes down to how secret you can keep it in the first place, to keep folk from even knowing about it in the first place. (see my sig/by-line). 
As a minor addition, there's the inevitable problem that, at some point, by accident or oversight, the item could be separated from the boat at some point where the folk remaining on the boat really need it to fly.
Refer to Constant Mystical Effect , page 168 ArM 05.
The ship itself, on the other hand, would be warped. You may very well end up with a literal Flying Dutchman. 
Hehe but a flying dutchman would be cool
Dont forget two thngs:
- the ship will be protected by a powerful aegis, so dispelling the flyinig-spell should be very hard, only extrem powerful beeings should be able do do this (like PeVi archmages) and changing into somthing other or using hedge magic on board should be impossible.
- Even if you remove the item: the ship wont crash into the ocean or on the land until the duration of the day spell ends!
But I think an item for some situations that is hold by a magus and that can enchanat the ship that it flys for Sun could be very useful.... but this would be keept secret.
Generaly I see it like chuchulainshound: to enchant a single, little item has far more advandages than enchanting a big item.
I add a thing to the ship:
Daedalus Little Helper: the Defiant
A small ship/a big lifeboat, capable of carrying 10 persons and a small load of goods, that flys at a speed of 20 miles per hour. A small scarab, build into the Defiant s it is invisibe to normal eyes enchants the ship with the a ReHe effect Flining the Defiant ReHe20 Touch, Sun, Individual, base 3, Size +1, constant effect device +5 levels
A spell that reduces every fire seems unneccesary for me, because the wood of the spell is already extremly non-flamable due to the MuHeTe spell.
Btw: Forrestal? :>
Security of the Falling Sky
Muto Herbam Effect:
Duration:Sun
Range: Touch
Target: Part
When set on a piece of wood (say the railing, or floor) and the command is given, the wood the object is sitting on (or pressed up against) will reshape itself around the items base (or top). A command will force the wood to reshape itself back to allow the item to be removed.
L:3 +1 touch, +2 Sun, +1
Level: 15
Freq: +1 two uses per day
Environ Trigger: +3
Final Level: 19
Thaumaturgical Transformation of Plants to Iron
as per Spell: page 137
When "Security of the Falling Sky" is used, the item uses this effect to strengthen wood.
Uses per day: 2 +1
Level: +3 Linked trigger
I could suggest other nasty things, but I'll let you fellas tear into these first... 
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