I've seen Honda put a 27mm carb on the early ATC250R and later moved to the 34mm on the more popular years. The mx 250's typically use 38mm, but 36mm is prevalent on trail worthy 250's. The cylinder is going to demand the same volume of air regardless of the carb size. The primary difference will be, as stated before, the velocity at which it is fed.
Larger sized carbs typically only provide enough velocity during the hi rpm's, making most of the power in the upper rpm's. They usually lack somewhat in the lower rpm's due to a lack of air velocity for those rpm's. Smaller carbs usually provide better velocity at lower rpm's generally providing better power in the lower rpm's but usually sacrificing power in the upper rpm's due to a velocity restriction.
So, it's a matter of finding the proper balance for your bikes power band and your riding style. I must say, the manufacturers do a pretty good job for the bikes primary intention and would be hesitant to change carb sizes. Changes to your motor can effect the optimal carb size, but I'm no expert on that. If you go to a larger sized carb, I'd consider putting a venturi divider on the motor side to help keep velocity up for the lower rpm's which will provide a better balance to the power output.
Basically, increasing carb size does not necessarily mean more power but more of a different distribution of power which may or may not be in balance with the engines needs. The 125's run 38mm yes, but they also develop their power at hi rpm's. A 250 running the same 38mm carb will have a better balanced power output, though typically will still see most of that power in the mid to upper rpm's. Having ridden an old yz490 using the stock 38mm carb, I find it has good power in the low & mid rpm's and falls a little from the top rpm's.
