It probably won't matter that much at all performance wise.

There are a million reasons why Windows doesn't clean up after itself well, and why temporary files, install files, and older system files just don't get cleaned up. It's why there is such a huge market in programs to clean up after windows.

It's not stuff you put in those directories, it's windows itself doing really bad housekeeping. With 60% of your space free, I wouldn't even think twice about ignoring the message.