In ECO mode... the vehicle goes skimpy on the AC as well as throttle and some other systems that affect MPG efficiency. I have no idea how the vehicle interprets how to manage the AC with S Mode with ECO enabled. So the question becomes in a tug of war between ECO and S mode.... how does the AC system fair in terms of settings and efficiency.
I do know that S Mode with ECO on will give you better throttle performance because I used to have ECO on all the time and would occasionally enter S Mode for some extra throttle performance. I have no idea how it handles the AC under those settings though.
Now days, I keep ECO off in town (where I do most of my driving) as I also found it tends to cause the battery to be under-charged on short trips (established through experimentation), which makes sense since the alternator charging the battery is a modest drain on fuel consumption.
For my personal tastes, Honda is just doing too many sneaky things behind the scenes with the various systems in the vehicle in order to eek out some more fuel economy. I just wish they would document them all so we can make informed choices and adjust settings and driving choices in an informed manner without having to conduct personal experiments.