The only part of the CPAP that they are interested in swabbing is the main machine, not your humidifier or mask. I think it's because it's too dense to see through on the x-ray. Most airports actually specify that you take it out and put it in a bin when entering security. This also helps you expedite your screening process by having it out ahead of time. If you're worried about them touching your mask you can put that in a ziploc bag so they don't have direct contact with it.
Also remember that it must always be in a CPAP specific case to be exempt from the 2 bag rule. You can't put it in a suitcase with other things and tell them that bag has medical equipment in it to qualify for carrying on an extra bag. Sounds like you're doing everything right by using the CPAP case and labeling it as such.
Hope it's helping your sleep apnea too!