I've used the Perfect IV codes on some trained pokemon on my team, I haven't used the EV codes on Generation 5 yet, but in Gen 4 I've always checked my EVs and deleted all of them before adding them, and they were allowed in Pokemon Battle Revolution(Even the ability hacks(I wanted a Speed Boost Yanmega) passed)
I tried a nature mod on a few pokemon but haven't tested them online(Its not working ), but if they were found as "illegal" can I just use the nature cheat to change them back to the original nature? (Making them legal again)