This is something that is tied up on the application server install. When you install, oracle would pick up the hostname.domain as your url. It all depends on the default hostname on the server. I encountered somewhat a similar problem on iAS 10g install, and the solution was to set the default hostname properly. If you are very desperate to change the host information, my suggestion is to consult the Oracle. Metalink has a script to change the hostname information for iAS. You may want to take a look into it to see what are all the XML files you have to make the changes on to.
You can delete the target in grid control, edit the agent targets.xml (take a backup first) and then bounce the agent and rediscover it in grid. Please note this may not work, the agent has a habit of rewriting parts of the targets.xml when you bounce it. Also, when you discover the target again in grid manually, i believe you can call it what you like. Try it out on a test server first.
I suspect a similar set of steps for database control, but I don't use it so couldn't be sure.