Why the hell did he even disappear? It was after a very ominous cutscene too.
Was Nomura setting something up that was eventually dropped when they decided to make BBS a prequel?
The secret ending shows one of the armored figures grabbing Way to the Dawn, which is supposed to be an evolution of Riku's soul eater sword and has a heartless symbol keychain (the symbol was created years after BBS). That keyblade shouldn't exist in the past and the whole sequence with the three keyblades was scrapped when BBS came out.
It seems that the secret video was originally hinting at KH3 but they changed it for KH2FM when they came up with the plot of BBS and decided to make it a prequel.