I don't understand. Then again, my brain does switch back and forth from academically smart to common sense smart. I'm weak on both, and I'm in the academic stage, so I dont quite understand.
Since the chaff grenades mess with radars and stuff (Just looked it up) and Reploids don't normally have radar and such I would say that Chaff Grenades would actually blind a reploid and ruin their navigational abilities.
I mean most video game characters are able to store items and weapons and pull them out of nowhere (Known as Hammer-Space.) So I don't think they don't really have anything to say except:
"Hey I wonder where all our stuff goes when we put it in [insert name of bag, or storage system here]. I mean literally we just put a freaking assault rifle in a bag along with one sword, and other large things and it just disappears until we need it! What's up with that?"
Do you really think I'm that stupid? *Walks into a door* Okay maybe I am that stupid...
The Mary Poppins bag theory would explain some of John's storage capabilities, but he does have a duffle bag strapped to his back.
EDIT: Oh, and about the Chaff, I actually found out that John's armor might be hardened against chaff.
(From the Wiki)
It is a sealed system, capable of extravehicular activity or operations in toxic atmosphere. It is hardened against EMP and radiation, and has filters that are completely effective at removing toxins and bacteria from local atmosphere.
Sometimes when you're driving down a road, a bug hits your windshield. It's ugly and unpleasant, but you just activate the wipers / cleaning fluid and it's gone in a few seconds. It's just part of driving down the road. You don't dwell on it, because that'd be silly. Bugs aren't worth the time.