Sorry I missed this, there was a couple days where I didn't get notices about new threads.
First, regarding the hole. it is supposed to be there and should not be plugged. You will see most skimmers use a union or oring seal to seat the cup. We use water as our seal and that is the point that the water height must be at to seal the cup, basically the weight of the water seals it. The hole keeps it at the correct level. Some bubbles will escape but if it is extreme the cup may not be installed in the center or fully seated. If you install it so this output is against the wall of the sump the water will trickle down the sump wall and the bubbles will be released before they hit the water and this will also minimize bubbles added by the splash.
If the skimmer is noisy, the pump is likely the culprit. Check that the bush bearing is fully inserted and make sure the pump is turned so its wider profile, the side the cord exits from faces down. This will minimize the contact with the base plate and body which may transmit more vibrational noise.