I don't agree that everything with an antenna is detrimental. I expect the rules apply to transmitters. It would be acceptable to use a shortwave or airband receiver with most airlines, despite the fact that the screening of the IF (intermediate frequency) stage of the set would be an unknown. The GPS is just another receiver, any radiation will be from the mixer circuits inside the unit and expected to be in the order of microwatts.
I agree until "tested" around the aircraft, results cannot be known, but we have often agreed to their use inflight with prior notice so we can watch out for glitches.
I would say that sensitive control and antenna cables in the aircraft are already screened and as long as you don't try to poke 5 watts of VHF around, they should not detect the small amount of RF generated by a handheld reciever. Interesting question though. As always, company policy or captains decision final.
Bob