I think you can replace the "glass" and it shouldn't be that expensive. For the Nokia 5800 it was around €15. However, as the N900 is so new, it might be hard to find spare parts.

I wonder if the screen protector is like the car seat protector. You end up having your seats material in pristine condition, but you never see them and you have been sitting on this awful protector all the time, which kind of defeats the purpose.

Yes, the screen in N900 will scratch in the long run and therefore the picture quality will suffer slightly. However, the screen protectors I have tried scratch much more easily and the picture quality will suffer quite considerably. Of course you could just keep changing the protector, but I feel that it will be eventually rather more expensive than simply have the "glass" replaced.

Well, that is at least my opinion.