In my recent test of scope/lasers on L weapons, out of 1000 shots I had 3 shots with a skillgain but no recorded damage. It is, as you say, impossible to know if those were real misses that received a skillgain, or (as I have thought since I first noticed them) actual hits that were somehow eaten by the server before they could deal damage. It for sure wasn't just lag, though.
Here's the formula for expected hitrate by HA:
avg hitrate=[(HA*0.011+.80)*100%]
So your hitrate with UL gun and no modifications should be (3.2*.011+.8)*100%, or 83.5%. Your scope/laser skillmod of 58% would increase your HA to 5.056, for an expected hitrate of 85.56%.
At least in records I have kept, I often have variation in skillgains of 10% on similar sized runs as you report. Thus it will be very difficult to notice a 2% increase in skills coming from your improved hitrate. You could count your hits if you want to test whether your hitrate is improved at all by the skillmod. This has been tested before, and expected gains were noticed on UL guns. But more testing never hurts!