Yeah I'm curious myself, but it could just me, minors not understanding, "Legal" pokemon in pkhex and using online with lets say incorrect ability, pokemon that stay in mega form, IV's & EV's totaled above the legal limit, people using mega evolutions that aren't even released yet or even the possibility of having mega stones in inventory that aren't meant to be there, with shiny pokemon it is hard to say as they couldn't tally how many shiny pokemon you have (Hatched, SOS chained or Wild Encounter shiny pokemon. I would say if you are worried about shiny pokemon made in pkhex just make them with a different OT & SID. as then it could of just been from Poke' Bank, GTS, Link Trade and lastly Wonder trade as that is what I have done.
I think they targeting people that do that do things that make it "unfair" to others in competitive play. After all my theory comes from the fact why not ban everyone that play online in general connecting online? and just the ones playing rating battles, I don't play rating battles because of the bans I have edited my save file and there is most likely no turning back to fix it.
a little offtopic but I also don't understand why people frown upon pkhex as It is a time saver for those who dont simply have the time to hatch thousands and thousands of eggs and then hope for correct natures. I occasionally try to do "LEGIT ones" but then it's even more time consuming to EV & IV train & with all correct moveset. I myself and really thankful for pkhex because I don't like sticking with certain pokemon for a long period of time. I will end it here as its not on topic related.
Thank you I believe this goes for everyone else but mostly TheSlayer for all your contribution you have ever made and Kaphotics for PKHEX being so user friendly. just wish there was a legal checker for all generation pokemon.