any contact with exposed cables WILL be a problem, either affecting braking/shifting or damaging the bags. most likely both. contact with cable housings shouldn't be a problem........after all, cables in housings are often run under handlebar tape without problems.

sandwiched between the frame and the frame bag should be fine. just check the curvy bits where the housing jumps between triangle tubes. loose/unsecure bag could pull cables out of alignment in the corner curves and affect braking/shifting.