Intellij Idea recommends to exclude directories related to project and IDE from MSE. I think that's a reasonable compromise between performance and security.
At the same those folders are probably the biggest backdoor into your system if you are a software developer, software developers are smart enough to not download crap from the internet, but they will gladly run npm install with full user privileges.
They once setup here the scanners to prevent modification of executable files. The linker called by GNU's GCC was...well...surprised.
Not a problem if you build the Windows stuff also on Linux.
