what protein skimming does is uses bubbles to collect whats called DOC
(dissolved organic compounds) they adhere to the microbubbles and float to the top of the skimmer where the bubbles burst and then are set into the collection cup of the skimmer. So the more bubbles you have the more ability there is to remove the docs before they break down in your tank and cause nitrate problems. The water in my skimmer is pushed out because the skimmed water is heavier and moves into the other chambers while the aerated water is still being skimmed. Its just like pushing water through anything its the force behind it that moves it. And no it wouldnt get clogged because there is a force coming out of the pipe and nothing really gets near it, not even my snails, they get blown off it.