1) Future of FNH is a 1.2 release in the not too distant future containing mostly bugfixes for 1.1. From there it's further advancement of the automapping API (making it smarter and easier to customise) and a general cleanup of the API. While that's happening we'll be tracking any new changes that've arrived in NH3.
2) There are no plans to integrate with NH proper. FNH can be considered a "contrib" project and will remain relatively independent.
3) There are a couple of forks out there with NH3 support, and we'll make an official release very soon.