He said he doesn't know how to work PC98 canon and characters into the Windows games, but not that PC98 things could never make a modern appearance. Alice and Yuuka are both from PC98, and even make references to PC98 events, effectively canonizing them.
Mima, or anyone else, could return one day, if ZUN decides he wants to use her and has an idea how. I wouldn't count on it ever happening, though.