Does the sub systems tab tell you that you have the gun installed (click on the button that says "deck gun 100%")? Check that first.
And just a shot in the dark here, try installing the rest of the Equipment_Upgrades mod in the appropriate order.
According to Sober that is:
Equipment_Upgrades_Fix_v1_4_byTheBeast
Equipment_Upgrades_Fix_v1_4_Patch_1
#Equipment_Upgrades_Fix_v1_4_Patch_1_HotFix
Equipment_Upgrades_Fix_v1_4_Patch_1 (available by date) V9 by sober
Fix Equipment_Upgrades Date Sober V9
And it's apparently recommended to be docked when you load these up, not sure why.
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