A new fix by meh321 for Skyrim Special Edition has been released, if his previous fixes are anything to go by this may well bloom into a few other fixes as time goes on.
SSE Fixes - Its currently in beta, but apparently fixes an SSE bug which "causes low FPS with many ESP or ESM plugins installed. Also adds option to enable OSAllocators like in vanilla Skyrim, but it's disabled by default because for me it lowered FPS slightly".
To test the issue :
I haven't tested it personally yet, but have no doubt meh321's results will prove true, thats an astonishing difference.
( I also do not have enough mods to make this problem manifest on my setup, so have never been aware of such a problem before now ).
So anyway, do we have a list of mods recommended in addition to the USSEP somewhere that this may be added to ?
Edit : It would not surprise me if this is also a Fallout 4 problem (it has already been mentioned that it is not a problem for Oldrim) Edit : Just saw a comment by Gamer Poets, he has seen someone test Fallout 4 with the 240 empty plugins test, and did not experience any reduction in FPS .. So this problem seems confined to Skyrim Special Edition.
Edit 2 : Ousnious has passed the info along to Bethesda, so possibility of it getting fixed in future .. maybe / maybe not / in the hands of The Nine