This question on Stack Overflowquestion on Stack Overflow suggests that deleting files should help. If you have multiple WYSIWYG editors, remove all that you don't need. Some of the editor plugins (like fckeditor) have an unbelievable number of files.
However, since it's shared hosting it's likely that the message is caused by the number of files across all the sites on the server. I would contact your host about it; they probably have too many sites on one server.