My results mirror this exactly. Not having to clean as often is a huge bonus in a long range coyote hunting rifle. Was to me anyways.My space gun has one five gallon bucket of brass through it. That's about 5k. Never shot anything but moly. I gave the 7.7 Kreiger the barrel a good scrubbing with Flitz and the barrel looked great. I took it to the range and shot a bunch of 1/4 inch'sh three shot groups. Still shoots incredibly well.
I have a 223 Ackley Remington barrel that probably has MORE than 5k on it. Same story.
So, no. No ill effects. I moly because it has always worked great. If it did something negative I wouldn't be using it after 30 years.
Moly bashing threads are second only to barrel cleaning threads. Like a plague. IMHO.
Paul