Well, one important point about using the trophy room is that we WOULD be able to access it, much more easily than anything in the Headmaster's office. Especially a suspicious Headmaster, if something dire is going on and we need help in a hurry. The staff could access it in an emergency, too, come to think of it. Or it might be a vehicle for exchanging messages. I don't think there are any portraits in there, or at least I don't remember any.

And the trophy room is central, too, rather than inside one of the Houses and so protected by passwords. It's just off the Great Hall--yet really tucked a bit out of the way and isn't visited very often. And all with the jogs and turns of the corridors right there, it's easy to slip into it unseen. It would be a discreet place to go to if there was some sort of ruckus. I'll bet no one was in there the night we helped Sarah Fawcett escaped, for example, but all of us were near it. If there was something in the plaque (or cup, or what have you) that could have helped her escape, that would be something.

We don't have any Emergency portkeys yet, do we? Dunno how you could plant one in the trophy room and not have Professor Dolohov detect it, though.