Naminé's name was derived after nami, a Japanese word meaning ocean wave. This is probably a reference to Kairi's name which means ocean or sea in kanji.

The connection between Naminé and Kairi is very deep seeing how Kairi's nobody is Naminé. That is probably how her name came to be. A wave is just a part of the ocean, just like how Naminé is just a part of Kairi. In the end waves just disappear back into the ocean, just like Naminé's destiny to merge back with Kairi and becoming whole again.