As long as you do it through WHM (WHM -> Account Functions -> Modify an Account), WHM will re-configure everything for you automatically. It may take a few moments before everything is completely done after you rename a user.
Just one that I can think of - and one you don''t see a lot. If you have a customer using a custom PHP or CGI application that references the absolute path (i.e. /home/oldname/public_html/blah and you change the username via the WHM interface, that application won't work properly anymore until you edit it to reflect /home/newname/public_html/blah.
This doesn't happen very often, but it does happen. And, it's important to note that it is _not_ something that Cpanel could possibly take into account. I have never encountered a problem changing the username, except in a rare case where a customer had a full server path coded in a script.
Not only that, but it changes the name of any databases you have, and database usernames, and prepends the new username to them.
So, you will need to edit all connect scripts on the site, if you use a mysql database.