But there are two points that work against them becoming 'atheists'.

One, Force-sensitives always feel the Force. It would be like trying to deny light exists.

Two, they were raised in the expectation that they were to serve -- but it is pretty clear from the get go that not all Younglings go on to become Knights -- and they know no other culture.

I think that more than a few of them might have turned Dark and served the Emperor willingly, though. That's a definite possibility.