I've flown GA for over 20 years, 135 and 91 professionally for half that, and nobody cares what the luggage rack has. Unless you're flying a Venezuelan-registered Lear into Ft Lauderdale and your paperwork is sketchy (this was a month or two ago), nobody cares. Signature at Boston still runs baggage through a metal detector but if you're voluntarily flying out of Sig-BOS, you have far greater judgment issues rthat what you're carrying. Enjoy the freedom and liberty that GA gives us.
As far as airline flying goes, if your carrier diverts to a non-friendly State, NJ, NY, CA, usual suspects, etc., people suggest to not take possession of firearms and keep it with the carrier to send to your final destination.