I would not keep your cover open because this is what Apple says:
Warning:
Always shut down the computer before opening it to avoid damaging its
internal components or the components you are installing. Do not open the computer
or attempt to install items inside it while it is on.
I have a Power Mac G5, i ran it with the cover open once, and then it just randomly got slower. I dusted it, and it got a little faster. I really don't think their is a problem with running it with the cover open, but I don't do it because Apple says not to.
Warning:
Always shut down the computer before opening it to avoid damaging its
internal components or the components you are installing. Do not open the computer
or attempt to install items inside it while it is on.
I have a Power Mac G5, i ran it with the cover open once, and then it just randomly got slower. I dusted it, and it got a little faster. I really don't think their is a problem with running it with the cover open, but I don't do it because Apple says not to.