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Whatever happened to the magic guns?
This answer is actually really boring - for the moment, they've just been put into storage as they're seen as too much of an advantage (they cross the border of what's "fair" - which admittedly is a fluid concept within the Agency).
Ryan tried them out and Jonesy salivated for a bit, but after that, just chucked in a box and forgotten.
Whether or not they surface at a later point is yet to be seen...