After seeing scattered reports, I tried this earlier and it didn't delete anything. City of Heroes was still listed as a game and it even launched the client. COH Subscriber Beta did disappear from the list after a launcher update, but it didn't remove any of the files.
Still, the safest thing to do is to simply delete the NCSoft launcher. It's possible that a future update could delete them, so better safe than sorry.
If you use the uninstall, be careful not to tell it to uninstall your games. Make a backup copy of your screenshots, demos, chat logs, costumes, etc. first just in case.