Yes they'd need to penetrate but as for the second one.... hmmm... depends how officious you want your Quaesitori to be. It could reasonably argued either way, which may drum up some interesting Tribunal meeting arguments, but I'd say it was no more scrying on a magus than if you tracked them in a purely mundane way.
As for penetration, you can have an effect just like Image of the Beast and not need it to penetrate. This would be like The Whole from the Part (HoH:TL pp.72). The base would then be higher, and the spell level might actually rise despite using R: Touch. But that seems like a fair trade-off anyway.
I would say that yes, they do need to penetrate Resistance (whether Parma or Magic Might).
And I would also say that yes, technically, they do constitute Scrying under the Code since you're using Magic and I believe that there have been canonical cases of someone doing something similar – using Intellego magic, not knowing that there was a magus in the vicinity, and they saw the magus via magic. Granted, there have been varying degrees of success (or failure) in prosecuting the violation at Tribunal, but it is still a technical violation, and that's even assuming that he let slip that he had seen a magus with his magic. If it were my magus, I would be inclined to tell the others that my spell failed for whatever reason, and try to pursue the investigation with mundane means since the Order, as far as I know, doesn't have a "Fruit of the Poisonous Tree" doctrine.
Yes, it is technically scrying if used to track a Bjornaer (or any other shape-shifted magus). Probably not particularly likely to be prosecuted --- depending on the context. Even if it was prosecuted, I think that if the casting magus could claim/argue "honest mistake" (as in he didn't know the target was a magus before he cast the spell), then he would just get a minor vis fine.
Unless you're playing a quaisitor with an obsession for following the letter of hermetic law, or you have such scrying on you, does it matter if it counts as scrying?
These sort of petty accidental violations of the code seem beneath the interest of magi, so I would see not motivation to press a charge at tribunal: "I accuse this magus of, 5 and half years ago, having scried on me by analyzing my tracks, when I travelled in heartbeast form. Although the scrying was accidental, as he had no way of knowing in advance that the tracks were not those of a mundane beast, and although no damage was done to me, I still believe he should be charged with a hermetic crime." Why wouldn't he get laughed out of tribunal?
Even if we suppose that this would be a valid case worth pursuing, or that the bjornaer and/or quasitor are petty and vindictive and would press the case regardless, how would they ever know that the magus committed a hermetic "crime" in the first place?