Thats a really good point.
NP Neducing BioPellets however seems to be more worried about excess bacteria then the lack of air.
"Quote"
We also suggest placing the outlet of the pellet filter in front of a protein skimmer, to limit the amount of bacteria entering the system. This has the additional benefit of increased gas exchange (CO2-removal and O2-addition). The pellets should never be used without sufficient aeration, as this may lead to low oxygen and pH levels, especially during night time. Proper aeration can be established with air pumps and protein skimmers.
http://npbiopellets.dvh-import.com/i...Important.html