The emp effect is to create a building constraint on particle cannon part. It does this in a similar way to the deck gun stun, creating an area around the PC that makes it heavily detrimental to place them too close together.
The second reason for the emp effect would be that supplying a tall energy weapon in the middle of a ship would likely be too safe and/or efficient with simply placing a reactor right next to it. By limiting how close to a reactor a PC can be placed it decreases its efficiency.
Some notes/thoughts about balance levers on this point:
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The specific range and amount of energy drain are simple levers to adjust the severity of the placement of this part.
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How the emp effect occurs could be a point of balance/thematic choice, in that the drain could occur over the duration of the gun firing rather than instantaneously like other current emp effects. (this could be some cool lightning effects while the weapon is firing)
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The emp on nearby reactors also could be used to limiting how fast the reload timing on PCs clumped around a reactor can be. (With a minimum speed of around the reactor's generate speed?)
tldr:
Emp effect creates limitations on placing particle cannons near to other particle cannons and near reactors.