So I usually like to set up my main base inside of a dungeon, since that means that I don't I have to spend forever building it (And because I like the way Ape dungeons look). I thought I killed every enemy in the miniknog tower I planned to use, but when I returned with building materials, I was attacked by a drone. Now, maybe I'd missed a drone, but I figured I'd ask: Do monsters respawn in dungeons? If so, then I guess I'll find an uninhabited garden world, and make a base there.
i would imagine that they normally do, as mobs normally respawn...wherever. you may try re-placing the background (knocking it down a bit at a time and putting it back up) that way the game recognizes it as a thing you built, and monsters won't spawn inside stuff you build. just make sure you get the background back solidly. it doesn't have to be the same, but don't leave gaps.
In my experience, they do not respawn for the most part. I once refurbished a Hylotl castle and converted it into a settlement, and did not witness any respawning mobs.
i strongly suspect that jonesy has aeons more starbound playtime than i do, so let's go with his answer
yea, once i lit everything up and cleaned, i didnt have any problems with that, my best bet would be to place light sources just in case