I suppose the information does have to go both ways, but the cached data shown on the maps is a slice (albeit one tailored to you) out of Apple's DB.

I'm sure Apple's DB can safely toss out any data even remotely associated with identifying a particular phone. In the end they have a huge map made up of geo-locations for hotspots and cell towers which they're storing, and not having to pay Skyhook for.

I don't have a problem with that. It's the same story for Skyhook and Google. Though I wouldn't be surprised to find out that Google's data includes some identifying bits. Of large companies, I don't trust any less than Google at this point.