It only trolls thumbnails when it detects new video files, and only scans those new files for thumbnails. It looks in the iPhoto library because there is video in there too.
2hr movies are BIG, and the IO for handling that is typically done on high performance arrays, not local HDDs. Its even worse if you're not working in a RAW mode, where the CPU/GPU is decoding, editing, and recoding the data on the fly.
If you were using iMovie right, or on the right hardware for the load, you would not be having these issues. If you're doing 2 hour features, you're already doing it wrong, iMovie is designed for shorts, not features (go buy FimMaker Pro).
iMovie on iPad is great for 10-25 minute clips. it;s not doing advanced editing oreffects, just simlpe audio balancing, transitions, and clipping. Even the iPhone 4 handles it just fine. My wife's 2 year old Macbook (and for that matter mom's 4 year old one) handles Hd editing in clips under 20-30 minutes just fine on laptop hard drives (clunky, but I/O, not CPU limited).