When I read this I thought I was going to burst out laughing. First of all, Square made the game, so when they create the guide, they'll know what was in the game to find. Secondly, the guide states that it lists every item, monster, etc. If it didn't, they could possibly get a lawsuit over a stupid little guide.
They aren't in Final Mix either... the ones in Final Mix are Diamond Dust and One Winged Angel. There might be another, but I'm not sure. Still doesn't add up to 3 'secret' keyblades though.
Fourth of all, the Ultima Keyblade is named Ultima for a reason. It pwns every other keyblade in each attribute, hence 'Ultimate' prefix(although Square has contributed to the coining of the word Ultima in the gaming buisness).
If you really want to get the keyblades, you have to be a decent hacker when it comes to gaming. The weapons they used aren't assigned any stats, so your hacking will just get you a different look on they keyblade. Then again, if you're a good enough hacker, almost anything is possible in gaming.