I think that was the peak of the after-school syndication run, with new episodes airing daily. It wasn't altogether uncommon back then for shows that aired daily to have very large episode orders. For example, the Filmation He-Man cartoon had 130 episodes split between only two Seasons. It felt like there were more Seasons because the show remained in syndicated reruns for nearly 5 years, but no, only two large Seasons.
I'd guess the TMNT situation was simply a mix between the rise in the Turtles' popularity combined with the fact of that's just how popular shows were made back then. I can see why the first two Seasons were smaller orders but once Turtlemania took off I can see why they'd want more episodes produced. Once the "fad" part cooled off, the Seasons went back to a more manageable size, especially once it became Saturday morning-exclusive later on.
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