…for example a Keeper turned face down via Camouflage or, in very early versions, Government Cover-Up or Secret Data.

A: Yes, you must count face-down Keepers when you are counting your Keepers in play. Though they do not count as “in play” for purposes of using powers or winning Goals (though you can usually reveal them at any time) you still own them as generic “Keepers” for the purposes of Limits.

If you have a number of Keepers hidden under another card, however, as with the Treasure Map in Pirate Fluxx (or the Secret Stash, a Stoner Fluxx promo), those are all counted as just “one Keeper” (the one Keeper showing on the top of the other card/s).