I think that's because, as our good buddy Demise said, I think it went like "The ones with the blood of the Goddess" or whatever. So only Link and Zelda... and Ganon, because Demise made it that way so he wouldn't die forever... Or something like that. So Link, Zelda, Ganon, and the occasional Beedle don't become ghosts because only they reincarnate... maybe.