I don't think Kairi remembers Aqua. She went through a big trauma as a child. If I'm correct, Kairi would have been 4 years old when she met Aqua. And though she saved her life, Kairi seemed to forget about it as soon as she saw her grandma again. Like with everything, the memories are locked in Kairi. I assume her memory may be jogged when she meets Aqua again.