I'll take a stab at this. I haven't recorded any Hauptwerk samples. However, I have recorded live pipe organ several times in a variety of venues, so may be able to provide some useful answers to your question.
Here are my thoughts about the Rode NT1a:
Advantages:
- relatively inexpensive
- very low self noise
- Rode has a good reputation for quality and consistency
Disadvantages:
- large diagram condenser, typically not as accurate across the frequency range as a small diaphragm condenser. Also, sdc's often enjoy a broader frequency range than ldc's. Note, however, that sufficient care must be taken to avoid or reduce/eliminate in post processing low frequency artifacts such as organ blower noise, heating/cooling system rumble, etc.
- cardioid (directional) pattern which boosts or cuts bass response depending on distance from source. In most situations, an omni (essentially non-directional) or at least wide-cardio are preferred in order to maintain the integrity of the bass frequencies. The caveats are that greater care is needed to preserve a stereo soundstage with omnis, and omnis may overemphasize the negative qualities of a bad room.
The other caution is that the mic preamp and recording circuitry can have as much if not more of an effect on the recorded sound as the mic being used. So care must be taken, for instance, to not use a noisy preamp or one that colors the sound excessively.