Actually I created the post first and then I read that post of yours and was like "oshit" :lol
Exactly, by all accounts they are dead, they don't have a functioning brain to affect.
Which makes it a plothole. It's not like they never introduced genjutsu before to not know how it works, it's just that knowing what we know about genjutsu and pain's bodies it doesn't add up.
Ow, this img is going to make some Pain/Nagato wankers and the six paths jutsu =/= six path =/= rinnegan fanbase so butthurt
They did have the chakra Nagato was sending them, but Nagato himself shouldn't had been affected by it (since his chakra in his own body shouldn't had been affected, therefore not putting him under the genjutsu).
Genjutsu affects the brain in the end, by manipulating the chakra that goes arround and in it, making the user see and feel whatever the caster wants. Since the bodies didn't have any functioning brain to begin with, this situation makes no sense.
Yes and no. Nagato does see and hear everything the bodies do, but he doesn't feel what they do (pain, discomfort, exhaustion, etc). Imagine this: a puppet master send chakra to the puppet via the threads ... if someone decides to cast a genjutsu on the puppet, would the puppet master be affected as well? no, right?.