Generally: no. Any difference that may exist is so terrifically minimal that you will never ever be able to detect it.
Longer answer: it depends on the filesystem of the underlying OS. PHP itself doesn't do much with directories, all it does is pass the file path through to the OS which handles the intricacies of retrieving files by their path. This may be slightly slower if the path is deeply nested, depending on whether the filesystem looks up directories in directories one by one and reads them from disk or not. Most likely that information is simply meta data in a table in memory, which means any path is lightning fast to look up and you'll never see any difference.