Gyrobot, it depends on the Johnson, who they work for, and what the exact wording of the mission was. Mr. J is a person, like any other, so what might set off some, won't be an issue to others. Can't make too big a call there. Who they work for, that's another kettle of fish. If the gang was targeted because they stole a shipment of Saeder-Krupp rifles, and they were being punished for the theft, then taking all those rifles and reselling them on the black market may just make you the next choice for punishment. If the gang was on the wrong side of a 'dispute' with the local Yaks, then they likely wouldn't have any problem with you selling the guns, especially if you gave Yak fences first refusal.
But really, in that case, it is the wording of the job that is most important. If Mr. J says to deliver the weapons to a certain place or person, then no looting the weapons in the crates. If Mr. J says 'destroy the weapons', then you destroy the weapons. Any looting of weapons should be limited to a rifle or two each, if that. Of course, commlinks (and any associated funds or paydata), personal weapons, and other gear you find on the guards is fair game, so long as it doesn't risk the run, and isn't something easily traced. But don't risk the run trying to do 'field surgery' to get the dead guys' cyber unless there's a compelling reason to leave no bodies behind. (And there generally isn't when smoking gangers in their own place.) Now, if Mr. J says that you should make the weapons 'disappear', or really says anything other than destroying them or delivering them, you've got the leeway to dispose of them how you see fit.
Knowing the limits on acceptable loot is just as important as knowing the Rules of Engagement regarding stealth and bodycounts. A good, professional team learns these things before setting out on the run. A group of jumped up gangers and washed out corpsec does whatever they want, and usually winds up either on suicide runs, on the wrong side of a double-cross, or not getting work.