The hole in the skimmer is probably the pipe to the bottom drain. Some pools have the bottom drain run to the skimmer and then from the skimmer to the pump. If it is not clogged, some water will be pulled from the bottom, up through the skimmer and circulated. If you manually push the weir (the skimmer door) closed, you should be able to detect if you get water coming from the bottom drain. Sorry, as my drain has never clogged, I can't help on unclogging the bottom drain.

If your pool is staying clear, I would not worry too much about not having the bottom drain functional. Some pools are built without one.