I think the problem with their health was partly that there were so many of them. They seem to get sent in the same numbers as normal ships, even tho they're much more powerful.
It may appear that way, but the AI does pay more for the more powerful ships. Basically directly connected with the ship cap on your side. So if the MkI fighter cap is 192, and the MkI tackle drone launcher cap is 8 (I forget what it would be then, but you get the idea), then a tackle drone launcher would cost the AI 24 times as much as a fighter of the same mark.
If you want to see the math, you can turn on Advanced Logging and check the logs for wave calculations, etc.
In this case, though, I'm not at all certain what mechanic you're encountering.
My guess is that you're attacking some planet that's at least somewhat important to the AI, so it's sending in the Special Forces. The SF, past a certain point in the game, is generally big enough to overwhelm a good-sized player attack if you don't do something clever to deal with them. And the SF does have a special place in its black heart for Tackle Drone Launchers, though it does pay the correct rate for them.
If you post a save we may be able to figure out why you're getting slammed with so many TDL's.
On the drones, they start losing health much faster when they've got something tractored (and the faster with the more stuff tractored), but perhaps not quick enough.
On the targeting, I did put flags on various drone types to discourage the autotargeting from them, but perhaps something is awry there.