Bah, I didn't use Dark Knight for any of the dungeons where enemies multiplied. Just bringa high-level Monk and you can kill almost anything in one attack.

Or use magic.

...BUT Iguess if you drew a run with no Monk or Black Mage or Geomancer or Summoner, you might be out of luck. Dunno, haven't tried it.
FF3 Dark Knight sucks, anyway.

But good point about the Mini/Toad dungeons. There are items that you can use to change yourselves to those statuses but I'm not sure if they are available at the time you do those dungeons.