Is it? Granted, I'm a heavy mod user myself for various games, but only created mods myself for Cities Skylines and Cities Skylines 2 so I guess I know that ecosystem the best, and yes, there been a few cases of malicious mods, but "heavily plagued"? What ecosystem are you talking about?
Just learned Nexus mods is also pretty good about handling anything that's virus like, most of my modding experience has been external to that though.
As an only-tangentially-related aside, the difficulty of making mods for Windows games work on Proton also bums me out.
I wish some kind of cross-platform, sandboxed modding ecosystem existed solving enough problems that most modders would prefer to use it. I'm not sure that's even possible, though.
The mod API should not have to do this anyway. The OS should do this. It is beyond belief that most operating systems just allow programs to do anything they want simply because they’re being executed.
And if the OS can’t do this, you run in a VM which nvidia disallow you to do in a performant way.