Sorry for the slow replies, been busy moving house this week.
They overlap a bit, but roughly: NightCap is for photography, True NightVision is more of a 'fun app'.
NightCap: Full res photos, tap-to-focus, flash control, exposure up to 1 second, manual exposure mode.
True NightVision: Low res photos (1280x720 on 4/4S, 640x480 on 3GS), up to 1s exposure (not automatic though, instead there are 'modes' going from 'action' (25fps for speed) to 'max' (1s exposure for stationary use), 8x zoom. It also has realtime image enhancement that works as an intensifier (somewhat similar to curves adjustment in photoshop) so it can 'see' in much darker conditions than NightCap. And there's a bunch of live filters like thermal vision (fake of course - people have assumed otherwise before!).
Basically, if you want it for photography you'd want NightCap from the two. There are odd occasions where you might want both. I've done some astrophotography with the iPhone, and I found TNV made a perfect "preview" of what the final image would be like, while NightCap was the obvious choice for the actual photos. NightCap in that situation could barely see the object I was trying to capture, TNV could see it quite easily after cranking up the enhancement.
Hmm... flash is actually a real pain to deal with! You're right, it is impossible to judge because as soon as it tries to take a photo with the flash enabled it also adjusts the exposure. A "flash preview" button that temporarily turns on the torch could help. The other option is to deal with flash manually, monitoring the camera so I can trigger the flash during exposure. Problem there is that the exposure is going to be a bit unpredictable as a result.
I'm going to have to experiment with this quite a bit to see what can be done.