So basically, assuming that the AIs will soon be able to easily bridge corporate system to system gaps - then absolutely no password or security system, including but not limited to 2-factor, is completely transparent to them. If they all have root then they all can probe any database and find all the keys for any encryption. No attacks necessary - they can just log in with the info they can access.

I could easily see the form of a SHTF scenario with AI that is technically quite possible:

AI cleans out and zeroes out every private, business and corporation money account worldwide. We'd sink to caveman level just as surely as a coronal mass ejection event.