Maybe that's how the other "non-merged" pools work, you don't know they are actually running merged mining, and they
do keep them...
Rhetorical: The hashrate of Namecoin is now about 40% of Bitcoin; do all the pools with merged mining add up to that?
40% sounds pretty close. BTC Guild + Slush + Eligius alone aren't far off from it. There certainly aren't any LARGE pools that are hiding merged mining as far as I can tell. You can check yourself though by looking at blocks solved by "non-merged" pools. You can't hide the fact that you're merged mining if you post which blocks your pool is finding.