When it was first envisioned, the folks behind the East Hampton RECenter hardly could have expected how popular it would eventually become. Now operated by the Y.M.C.A., hundreds of people pass through its doors every day it is open, many of them headed for the center’s two swimming pools. The 300 or so swimmers there on a peak day, as estimated recently by the Y.M.C.A. director, apparently overtax the pools’ filtration and ventilation systems frequently, raising the likelihood of health risks for those who swim and work there.