A quick glace at the lazy man's online encyclopedia says that the difference between the -I and -II is the ability for the -II to carry a pair of 250 kg bombs. I wonder if it carried anything smaller?
If that is the only difference between the -I and the -II then I can see why HTC went with the -II.
That's the problem with a quick and lazy glance. There were many differences. Not the least of which was the wings had a tendency to break under bombload on the -I, so were significantly reinforced on the -II to be able to carry bombs.
Other changes include raising the cockpit, changing shape of the canopy, different engine and 3 blade prop with much more horsepower and +20mph speed, different cowling for said engine, shorter wings for higher speeds at lower alts, some pilot armor and fuel tank armor, ability to carry bombs (as mentioned) but also repositioned bomb racks.
As for the -I, it never had 2x7mm outside of prototypes or second-rate (non-combat) training planes. Almost every Ki-43-I that ever flew had the 1x7mm and 1x12.7mm combination. There is only one example of 2x12.7mm and it may have very well been a prototype in field testing, because it had no squadron markings or affiliation at the time it was encountered.
The -II may have technically had 2x12.7mm but there is some doubt as to whether these were kept. Much like gondolas on 109K-4s, it may have come from the factory that way, but was changed before being given to the pilots. As a whole the ammo expenditures still list 7mm ammo at a rate to suggest Ki-43s continued to use 1 of each gun well into the war when units started being replaced with more advanced fighters.
The 12.7mm was more than likely to explode in the barrel and blow your engine half to hell than it was to damage the enemy. In fact many wrecks have a steel plate inside the blast tube for the single 12.7mm because it was more likely to explode after leaving the barrel and they wanted to stop the explosion from damaging the plane that fired the round. It was an entirely unloved and unreliable weapon, so pilots kept the single 7mm to finish their kills if something happened to the 12.7mm (more than likely).
