Oh, balderdash. "Koopa Troopa" sounds silly, and most people find that all Koopas are enemies, thus, in their mind they belong under one banner. Also, we call people in the army just that--people. Koopas, being a non-human race, can collectively be called Koopas, even if they aren't employed by Bowser.
Hmm... On further consideration, I became less confused by Glorb. Here is my final answer. Sure, they're called Koopa Troopas formally, but Koopas is not so truncated to the point where it has little meaning.