If I understand you correctly you have a ceiling footprint of 12"x16" and a height of 36".
Mark is right about the heat pads or tape in this application - just forget it, immediately. Conduction (as in contact- or belly-heat) is simply not the right physics. You need radiation, with overhead heat. You say you don't want visual heat, so you need to go invisible, or infra-red (IR).
(I suppose if one were really hung up on conduction for arboreals, one could get cute/fancy with heated perches, using heat tape, heat cable, or heated pumped fluid in some sort of plumbing, but...ugh. Lots of time, some money, and probably you'd scrap the whole idea and come back to IR heat after about 6 months anyway. Maybe after cooking some snake bellies.)
With IR heat, either CHE or RHP is the answer. (Again, Mark is right.) Either one will ABSOLUTELY REQUIRE thermostatic or rheostatic control. RHPs are (to me) nicer to look at because they don't require screening to prevent contact burns. Since you have RHPs already, and for other reasons that will be explained below, I recommend this route for your problem (I'm using that word in an engineering sense, not a pop-pejorative sense. Engineers enjoy problems, they're like a puzzle or brain-game.)
Barring the RHP route, if you wanted to go low-wattage CHE instead you could "just" wire & mount a socket fixture in each cage's insulated (e.g., with reflectix) ceiling, frame out a portion of the top of the cage to hold the LED and CHE, and screen it. You'd probably want a hinged drop-down screen door so you could periodically fuss with the light and heater without ripping your screen (although both CHE and LED are good low-maintenance technologies). If all this crap is above the translucent front (and sides?) of your cage, no problem. Otherwise you're looking at it. Don't know if that's an issue; I wouldn't want to look at it myself. I find the best part of arboreals is the aesthetic plasticity or freedom you have with them - they don't beat hell out of their cages so you can really make a gorgeous habitat for them. I like to hide my plumbing, wiring, etc...
Um...I don't understand you saying you don't want the snakes to go down if they need to cool off. It's what they'll have to do, and they will, trust me. Just ensure there's a gradient. That is super easy with radiant heat and a tall cage (it would be virtually impossible to not have a gradient). You could easily (e.g.) have a 95F basking perch/branch right below the heater, several cooler perches a bit lower, and a substrate surface 30" from the heater that's around 75F (or whatever the ambient room temp is...).
Aside - I find integral cage-stacks a hassle. In the environmental control especially. I prefer to have each cage independently heated and lit (no shared walls or air space), well-insulated, and in a rather cool room. I don't like the temperature of lower cages to drive that of higher cages. In your case some reflectix on the ceiling of the lower cage, and to a lesser extent some deep substrate in the upper cage, might be helpful. (I'm assuming with 36" height you only have 2 cages high.)
Best of luck with this technical situation. In several aspects of their husbandry (housing, environmental control, feeding, human safety) arboreals require a substantially higher level of skill, and more time, care, and dedication than terrestrials in my experience. Keeper mistakes manifest in things like stuck sheds, respiratory ailments, anorexia, obesity, increased experience with veterinary medicine, bitten keepers, etc etc.
Cheers,
Jimi