Even when a seahorse eats the food, you still have lots of organic matter left over. According to one article I read, up to 1/3 of the food eaten due to the inefficient mechanical and biological processes of the seahorse. Watch the seahorses when they eat, it looks like smoke coming out their head. That is very fine food particles from the maceration process of the snicking. It can be roughly 8 % of the food taken in. Then due to the lack of a true stomach and the fast transit time of the food through the digestive system (roughly 10 hours or so), roughly 1/4 of the food doesn't get fully digested. Because of these inefficiencies, seahorses typically need to ingest more food per weight than many fish to be properly fed.
So to the original question, yes both an oversized protein skimmer and larger water volume are good. The more mechanical filtration you run, the less there is for the biological processes. Much of the organic matter is too small for the clean up crew, though the clean up crew is good for uneaten food.