Kids watching Saturday morning cartoons were not considered a very discriminating audience. Short seasons, frequent repeats and re-bundling old product were pretty common for that segment of TV.
And, it's far from uncommon. Twenty years later Batman: The Animated series did the same thing. Also, although I don't know this for a fact, I think it's sister shows, Superman and Justice League did this too.
They were all Warner Bros. productions, and the WB tends to get a lot of mileage out of their animated shows, even putting them into syndication.
Most old cartoons are still available through syndication--including Star Trek TAS--for any TV network or local channel that wants them.