I went to the Super Duper Mart and cleared all the ghouls long before I found Tenpines Bluff.

I now have a mission 'Ghoul Problem at Tenpines Bluff' that requires me to clear the ghouls from Super Duper Mart to complete.

I went there and found that a lot of the ghouls had re-spawned, and much of the loot had re-appeared (in the safes and boxes mainly).

I have killed all the ghouls again, but the mission does not complete. I suspect that I need to kill a certain number of ghouls to complete, but not enough re-spawned to achieve that.

Any idea how I can complete this mission?

Ouch, this has happened to me with Concord, I killed the Raiders after I was told to use the Power Armor, but before I put it on. The only way I could fix it was to load a save from before I got the quest and did it all over again.

Your right in that the game probably has a tally of how many ghouls you kill in that location while the quest is active. So, wait in game for 73 hours (if that is the timer on respawns in this game) and go back and kill some more. I also wonder if you can abandon a quest in this game...

You only need to kill one specific Ghoul, the one the quest marker points to. The quest should be completable as long as you have a quest marker.