It's a public rule. Not a hidden DMG that by secrecy suggests to a GM that they should be sneaky, but a public rule explaining consequences that can exist. The players will be aware of the rule and can decide with the GM how they're going to play it out. If you don't trust GMs, honestly, given how it's Shadowrun? You might as well throw out the entire book and walk away from the entire setting altogether. From 'Johnsons may betray runners', to 'the enemy you kill may have allies that get pissed at you in return', if you're worried a GM will not be able to handle it, then the entire Shadowrun setting is nothing but a trap. This individual rule is nothing but a blip, a mere molehill, not the mountain you're treating it as.
Bad GMs are universal. But a book explaining to both players and GMs what the consequences can be, is not something sinister that pollutes GM minds, it's a proper guide explaining that treason exists. The GM that unfairly throws that around is the problem, not the system that offers guidelines. Or is D&D broken for having traps, which GMs can use to completely wipe players? Is Vampire broken because a Mage can butcher an entire party? Nobody's shouting at D&D for Tomb of Horrors existing, so nobody should shout at Shadowrun for making clear to players and GMs alike that cased ammo is a liability.