Not everything in /usr/bin is a symlink. Many of them are the actual executables. A link only exists if the actual file is in a different directory not in your PATH. The PATH is the list of directories the shell searches when you type a command, BTW. /usr/bin is almost always in the PATH, so many programs just link there as an easy way to make sure the system can find them.
Try using "file /usr/bin/opera" to see what kind of file it actually is.
In any case, since it's seems to be there, and it's in your PATH, that doesn't seem to be the problem. It must lie somewhere else along the line. I'm afraid I don't know how to help you with that.
You might try uninstalling everything using the purge option and then reinstalling it again (be sure to back up your profile settings first). That might set everything back properly.
"/user/bin/opera" in the command line or the KMenu command should work to launch it in any case.