You've got that right, CtB -- Kindle for iOS is a sub-par product, and the inability to export highlights and notes is one of the major flaws in it. There's just no way around that currently.
If you need to export your annotations fom books you read on the iPad (as I need them), I suggest for you to convert (for example, in Calibre) your books from MOBI to EPUB and read them in the Marvin app, which is the best app to read books on the iPad. Marvin allows you to export your highlights and notes with a single tap of your finger, in an XHTML file. It's much better than the hardware Kindle's snippets file. I'm in the same pickle as you are -- I read books on hardware Kindles in daytime, and in Marvin on the iPad after it gets dark, so I end up with two sets of highlights/annotations, but there's just no way around that currently.