There was a rumor on an Episode II/Episode III board that I used to go on that said Naboo would be destroyed and turned into the swampland Dagobah. Personally I thought that was waaaaaaaaaaay too farfetched to be true (just like the ppl who for some reason believe w/ all their souls that Palpatine is not Sidious).
I may be wrong, but I think the reason Naboo is never seen or mentioned in the OT is because it is the planet that Palpatine comes from, and he does everything in his power to disassociate himself from his life pre-Empire, including leaving many areas of Naboo in ruins as a means of making sure the planet is more or less unattatched to any part of the star wars galaxy. I seem to remember reading recently that Vader is sent there to wipe out any connections to Palpatine and pretty much make sure that Naboo is no threat.
On a related note, Naboo is one of the planets featured in "Star Wars Galaxies" which is set, I think, during the time period btween movies 4 and 5 - so it almost certainly isn't destroyed. There are pictures on the website of AT-AT machines walking through Naboo swamps and as part of Naboo sceneries, so perhaps (like many planets during the Empire's reign) Naboo is under Empire control. It is likely that the planet is very quiet and peaceful, and unimportant - which is why it is never mentioned.