Because when it comes to higher level content using them is suicide. Plus Sniper rifles do 10 times more damage
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This is exactly what i was saying from the release of the game to December when DLC came out. They're extremely powerful if used on enemies that are already in your face (like a surprise Minoturd in VoG for example), especially the ones with fast fire rate (for maximum stun capabilities) and 6 rounds mag. Nightfall is the only content in the game i wouldn't suggest using a shotty because.... well, its kinda obvious but its better not be in the melee range EVER.
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Yes they do work if you have a void shotgun in VOG but to be honest you're still better with a sniper rifle for most of it. The only place I'd consider a shotgun over a sniper was if I was keeping a portal open at gatekeeper. Thats about it or maybe the confluxes but I'd be swapping to a sniper straight after because of the hobgoblins.