Can you "Search" on the iPad and find the app? If you can, iOS knows it's there and it might simply be in a folder you don't expect it to be in... Not invisible, just misplaced...
If you connect to iTunes and use it to rearrange the icons on each screen, I find that sometimes it easier to find a lost app that way.
I have a friend whose kids move all of her apps around and put them in folders where she can never find them... she has to do this rearrangement all the time.
-t