Well, it shouldn't cause a problem with your fonts, but if you want the error message to disappear, you can make sure the appropriate directories are in /System/Settings/fonts/fonts.conf. Here's what a section of mine near the top looks like:
<!-- Font directory list --> <dir>/usr/share/fonts</dir> <dir>~/.fonts</dir> <cachedir>/System/Variable/cache/fontconfig</cachedir> <cachedir>~/.fontconfig</cachedir>
The dir lines were already there in my version of fontconfig, but the cachedir lines were missing, and I think that's what was generating the warnings for me. If your fonts.conf doesn't have any lines like that, try adding them and see if it fixes it.
(Really, if you add anything, it should be in local.conf, as a comment at the top of fonts.conf suggests. That way you won't lose the changes the next time you update fontconfig if you take the new fonts.conf.)