This is the answer. Pure magic with a single line of code. Awesome work, jamiech1.
For those looking, do this:
Locate your MODS folder containing the zip file of Mining_Drones_2.0.0 (typically C:\Users\ YOUR USER NAME \AppData\Roaming\Factorio\mods.
Open the zip using most Zip programs, go to data\entities\mining_drone\mining_drone_entity.lua , then open it.
Towards the end of the file, you will see
corpse.name = bot_name.."-corpse"
add this just below it. Making sure the indentation is the same:
corpse.time_to_live = 6000
This adds an expiration for the drone corpses of 6 seconds (the number is based on milliseconds). Adjust as you see fit. Now instead of Factorio tracking each unfortunate deceased drone, they will be eliminated from existence, no longer tracked, and freeing up precious factory compute power. My own experience took me back to 60/60 FPS/UPS when it had slowly been sinking to 30/50.
Server setup note: both the server and the client MUST have the same modified file in place. I experienced issues when I did not properly indent the file, as well as using different Zip programs. I resolved this by just editing on one machine and copying that to the other. Specifically, edited on the server (Debian) and copied to my Windows computers.
I'll be suggesting this on Github for future versions as well. Thanks again!