It doesn’t have anything to do with the distro. With that many files, you’re torturing the hell out of your disks, and your machine’s memory. Depending on how the code is written, it depends on if this is a filesystem scan of the folders that are then imported to a local db which is looked up to go back and find the found files, or a simple approach which is to just scan the directory every time you go to open something.
I’d really think about properly organizing your files. If that’s not an option, you can dig into the settings or code and find the hard limits set (probably for a good reason) on the number of files being scanned or imported.