If you're talking PC only, you could just move the apps out of the iTunes folder so it doesn't know they're there, I guess. Why not just update them, though, or delete them? Either you're going to use them at some point so they might as well be updated, or you're not going to use them and so you may as well delete them.
If I choose the "hide" option in the App Store "purchased" tab do they stop appearing from my update list?
Honestly, everything to do with iTunes is a complete mess.