I also had this problem for a very long time.
My scenario:
I killed the dremora once. Then, they respawned after 2 in game days. I killed them again.
Then, they respawned again after 2 in game days. I killed them again.
After that third time of killing them, I never saw them again.
Today I finally ran into them again. I was so shocked and excited. I've heard that it takes 44 in game days for them to respawn, but it honestly felt more like 50 or 60.
So, if you are mad that they aren't respawning, be assured that they will come back. It will just take a VERY LONG TIME.
While you wait, you can revisit the Shrine for it's sweet loot. The loot respawns consistently.

