Well, the best suggestion I have would simply be to “ignore the folder”. ??
Realistically, theme-check is naive. On the whole, I’d prefer it to stay that way, given the intended audience. Better to throw an invalid warning that a smart reviewer can ignore than to hide a real warning which needs to be fixed.
If this folder is going into the theme ZIP file that will be released, then it’s valid and should be fixed. If that folder won’t be in the theme’s ZIP, then it won’t come up when the theme is uploaded or reviewed anyway (because it won’t be part of the theme anymore), and so it doesn’t matter. The only place this warning will appear is in your dev environment, and you can ignore it… or change the code to not read that folder for your own copy. I just don’t see that giving theme authors a way for the code to blanket ignore whole directories makes any sense on our end.
Note that I don’t use Grunt, and while I could make it ignore “node-modules” easily enough, I’d also have to put in code that deletes that directory outright in any uploaded theme if I did so (like it does for /.svn et al). Is this code that shouldn’t be in the released theme?