A6Ms actually handled altitude pretty well, particularly the A6M3 ans A6M5. They handle it better than the early European fighters in general.
Where did you get the idea they were designed for low altitude?
They certainly didn't gain anything over 20K and by 15K, speed improvement stops and climb rate drops. They may have not been made by the designers to be a low alt fighter, but they were definately better down low and slow where they outturned everything. Heck, if you were to take a Zeke up to 20k, all you have to do is point your nose down and he won't be able to follow you.
While altitude does help, with the Zeke, it offers too little for the price you have to pay. You lose climb rate, speed, and practically every plane can outdive you should they get in trouble.