In many ways I'd say that, because of the general belief and understanding that the Devah are very real, and that their powers can actually be seen to manifest at times (at least according to many), they are as revered as one's own parents might be, but with a LOT more power...an a great deal more subtle influence and presence... What this means is that characters and NPCs choosing not to show reverence will be chided by their peers, and warned that the Devah will surely show disfavor because of such behaviors... Such characters might be called lazy or worse, but because it's assumed the Devah are real, it's also assumed that They will handle such apathy as They see fit...

Now, of course, a GM might choose to actually have such events occur as bouts of ill-luck or other drama, or the GM might choose to have others treat that character with even harsher sentiments, with such spiritually apathetic characters or NPCs ending up being shunned or even ostracized from a community entirely... That should all depend on whether the particular region they are in is particularly zealous or not (as determined by the general descriptions of a place and the GM's whim), and how blatant a character is in their behaviors (i.e, are they "snubbing" religion openly and purposefully offending those around them with their antics, or are they merely quietly abstaining and making no big deal about it)...

As far as Nilam is concerned, it's less that they are "apathetic' and more, as you said, "agnostic" in some circles... Specifically the circle of scholars attached to the Academy of Nilam, who don't necessarily "dis-believe", but instead sometimes question the often "spiritually-depicted" elements of the natural universe these scholars study... They may still believe in the Devah, but they are not as willing to explain away all things as if the Devah are responsible...and may suggest things out of mere curiosity that the very devout might take offense at, at times, or even find heretical and worthy of punishment...

This has been used as a wonderful means of story-driven conflict in my games on a variety of occasions....

Regarding the disregard of morning/ evening prayers many would likely associate any ill fortune that befalls a character as direct proof of the disfavor of the DEVAH. In the world of the false dawn even the many things which in our world seem normal are in fact influenced by unseen forces behind the scenes and any character from this world would have a view of reality which supports this fact.
I have enjoyed all of our adventures in Nilam because of the fact that knowledge itself is often more free flowing within its bonds, even being able to locate an individual willing to speak about taboo subjects can be difficult in other less enlightened regions, but not so in Nilam, where the exchange of knowledge is itself the greatest commodity...