Answering your questions in turn:
Yes, you would have to bring Circuit #2 up to Code if you altered it. The applicable provision is actually E3401.4 of the International Residential Code as your jurisdiction doesn't use the Annex H model legislation to adopt the NEC.
The primary hazard the current wiring poses is that tripping Bathroom 1's GFCI turns the lights out on the unsuspecting occupant of Bathroom 2, which could lead to a minor disaster (say involving a hot curling iron, or stumbling and falling in the shower in the dark).
Adding the fans to circuit #1 isn't a problem, by Code -- bathroom outlets other than the required receptacles serving the countertops can be on any general-use branch circuit. With a fair bit of rewiring, though, it's possible to juggle things so that the bathroom lights and non-bathroom receptacles move to circuit #1 while the bathroom receptacles stay on circuit #2, which would make things almost fully Code-compliant (bathroom #3 would need to be addressed separately, but that's simply a matter of putting a new breaker in the panel and moving bathroom #3's homerun to it, based on your diagrams).