I'm not the best person to tell you about these issues, but I'll give it a shot

The choice you need to do is choose between Qt and GTK+. Latter is the native UI library used for applications. I wouldn't say that Qt is integrated with Hildon, Qt supports different styles for same application, and for Maemo 5 Qt style looks like native application.

For accessing phone functionality you will use Maemo 5 API and DBUS signalling.

edit: Also don't forget Python when starting application development.