Hi Andreas,
We have seen in the past some cases that cause Reduce to go into an infinite loop, which I thought had been corrected, but perhaps your model has found a corner-case that I have not considered. NCS vs. no NCS is not the direct problem, it likely has to do with a particular set of coordinate positions that you are reaching during refinement which causes the hydrogen position determination to end up in either an infinite loop, or just an optimization that isn't tractable in a reasonable amount of time. Hydrogens are added for both NQH flips and for clashscore calculation if your input model does not have them.
Would you be willing to send me your files (off list) for debugging purposes? If I can recreate the behavior here, I'll be able to figure out exactly where Reduce is getting hung up.
Thanks,
Jeff