Thing is, hit probability now DOESN'T depend on the opposing team's combat stats. The side with twice as many ships hits twice as often, which compensates for only doing half as much damage per hit. If you bring three times as many ships, each of which hit half as hard, you will inflict 1.5 times more damage on the enemy. So you're right about the effects of one change to the combat engine, but there's a second change which would appear to cancel out the first change.
In other words...
If two ships with Combat 6 duel for 30 rounds, they each hit 15 times for 6X damage per shot (where X is some average expected amount of damage). Each side dishes out 90X damage (ignoring evasion).
If one ship with Combat 6 fights two ships with Combat 3 for 30 rounds, the heavy hitter only hits 10 times out of 30. It still does 6X damage per shot, but that only adds up to 60X damage. Meanwhile, the Combat 3 ships score 20 of the 30 hits, and dish out 20*3X equals 60X damage. The results are still a tie (although interestingly, this suggests that the battle will take longer to be resolved).
If one ship with Combat 6 fights THREE ships with Combat 3, then the heavy hitter only hits (on average) 30/4 = 7.5 times. It's doing (on average) 7.5*6 = 45X damage. The smaller ships hit (on average) 22.5 times, delivering (on average) 67.5X damage.
So in the long run, 3*3 still turns out to be 50% larger than 1*6, which is exactly what you'd predict.