Number of outlets on air pump affecting air output?

I would say no. If only 1 line is being used, then the excess air that is spread across the other 3 lines would end up being forced through the only open line. A caveat to this is if the pump has internal piping to avoid this situation and would just let the excess air out beneath the unit (for example).

I’d just recommend connecting the 3 closed lines to a single tube and then using that, or more ideally, downsizing the unit to just have the number of open ports you would need to use in your setup.

Nah, bro, it ain't the same. If you got 4 outlets on a pump and only 1 open, the air gonna be forced through that one open line, makin' it way stronger. Unless the pump's got some internal pipes to release the excess air. But honestly, it's better to just connect the closed lines together or get a pump with the right number of open ports for your setup. Keep it simple, man.