The WIKI says the -1A's eny is 15, but at any rate, you don't think 1 20mm with 120 rounds, and 2 weak 12.7's with 600 rounds compared to 4 .50's with 1600 rounds isn't reason enough for the difference?
The AH Wiki is outdated.
Consider a few advantages the 1A has over the Yak:
The 1A is far better at BnZ gunnery and is the ride of choice for some big time pickers. The Yak cannot afford to spew out rounds and needs to saddle up, if only briefly, to make a kill. This puts the Yak in a more dangerous position for every kill, because the chance of getting picked is higher.
The 1A is far better at killing bombers, which typically yields a better K/D than achieved versus other fighters.
The 1A also carries a 1,000 lb bomb, resulting in some EZ-mode GV kills, which is another way to boost the model's K/D.
And yet, they yield the same results. One is 12 ENY and the other is 18. Over the years, planes have had their values adjusted and this is a case where it makes sense for the Yak's to be lowered.