My friends and I are running a MC Eternal server for ourselves and when running lag goggles we notice that clams are the mob causing the most lag and a significant enough amount of it that we want to disable them as we have no use for them. When I went into the config and set their spawning to false, and then down to the bottom and set the spawn rate to 0 it had no effect and they were still spawning, Our host is Bisect Hosting if that makes any difference.

Did you kill all the existing clams first after disabling their spawn?

Unfortunately, lag goggles aren't a reliable way to determine lag. I'd recommend installing spark and doing an actual profile on the server to determine what is causing the lag.