The "Dagobah is Naboo" theory has been around for a while (check aldera.net), and it has been debunked by the Star Map available in every NJO novel, with an updated one in some of the new AOTC books. If you look, you'll see that Dagobah is pretty far from Naboo, closer to the Sluis Van system. Naboo, on the other hand, is closer to Tatooine. My guess is that Vader or the Emperor levelled Naboo, or it was nearly destroyed by the Clone Wars.
"The whole starfleet couldn't destroy a planet; it'd take a thousand ships with more firepower than I've..." -Han ANH
"Hide a stone among stones and a man among men." General Rokurota, "The Hidden Fortress"