Okay, the answer turned out to be simple: Indeed the ods.cfg file in the /var/opt/NAI/LinuxShield/etc directory was the correct location.
The issue was that we had both an nailsd.profile.ODS.filter.N.X and nailsd.profile.ODS_1.filter.N.X entries. I had added my exclusions to the ODS_1.filter entries, but that was not what the Web Interface would display when it was started. I added my entries to the ODS.filter properties and all was resolved.
I still don't understand what the ODS_1 is. Is it another profile? Why can't I see it from my Web interface? Is it in error to have it there?