If your assemblies are that large, I'd look elsewhere. We're using Inventor on 5-7,000 part assemblies and the biggest problem is getting assembly drawings completed once you have the modeling done. Inventor just crashes constantly when trying to detail stuff this big. We've got great...
The hole feature doesn't work for NPT threads. To create these you need to extrude-cut a circular sketch with a taper (NPT is 1° 47'). Then select the thread feature and pick the hole. NPT values will show up.
