Okay, so it is indeed intended that there are less blights of each type than there possibly could spawn?
With no token limits, the theoretical maximum that could spawn is enormous; about 24-28 for most blights. There was no way we were including that many tokens in the game!
The maximums also have some relevance for game balance; some enforced variety prevents the most extreme good/bad cases and gives you some choice over what threats to face. The most important case is the Nexus in the fourth expansion, which only has one copy, because with two of them you could theoretically make a circle of blights protecting each other that would make it impossible to destroy them.