without a doubt
If Square Enix intends to keep Sora the main character of the story, Kairi is destined to show up in the third game in the series. Afterall, she is his love interest, and one of the Destiny Trio. They can't leave her out. But what role would she play? We know now she has a keyblade, though why is yet to be told. She is more than likely to be potrayed as the fighting girl rather than the one that needs protecting, though might be kidnapped again, as she'd be the easiest target to make Sora mad. Either way, she might be in the main party; the main party may consist of Sora/Riku/Kairi. It all depends on Square.According to what I know of the ending, one of the armoured figures resembles being female, which may make this being Kairi. One of the 'extras' in Final Mix is a shot of one of the knights with the faceplate off. Brown hair, blue eyes. Remind you of someone? If that is indeed Sora, then this may be Kairi, and would prove a point she is due for a bigger, more in-plot role rather than behind the scenes.
And lets not forget the actual ending of KH2. A letter is found: and as Kairi says to Sora - 'if one of us goes, we all go'. So maybe, they'll all go to fufill his mission. I doubt Kairi would agree to staying behind again, anyway, and if she was told to, she'd probably follow. We'll have to wait and see...
However, from what I know of the secret ending of Final Mix+. The only clear thing about it is the fact Mickey appears for a few seconds of this five minute sequence which gives a lot of speculation. One of the knights looks like either Roxas or Sora - and then there's blue haired - girl? or, it may be a guy. I'm not sure. But either way. It's not Kairi. My personal views are this is a long time ago prior to the first two Kingdom Hearts games and about the keyblade war. Or, it could be right after the second, concidering Mickey is there - he sent a letter to the threesome, right? So perhaps, maybe, just maybe, that was what the letter was about. To go there and fight. Or maybe the ending has nothing to do with this saga of KH, and could just be an entirely different one altogether.