No it isn't, since you can't even see the port. What you CAN see is the cable going to the port, but if that cable annoys you, then you have a REALLY simple solution to the problem: Don't use the extra port.
It's huge if you only have a one computer. If you have more than one, you are pretty much screwed. You COULD have it both ways. Have the current setup with the cable, and in addition have a vacant DVI-port on the monitor. If the extra port is not needed, no problem. It would not cause any extra clutter. But if someone needs that extra port, it would be there. Right now people who need more than one port need to look elsewhere for their monitors.