This problem can be worked-around by saving the game and replacing the line
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<Reactor recharge="20.000000" limit="140"/>
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<Reactor recharge="1000.000000" limit="1400"/>
Recharge values below 500 don't seem to help at all; a value of 1000 is required for the guns to work if one mounts an ECM unit in addition to the 4/3 shield.
I'm fairly new to Vegastrike so I'm not familiar enough with the source to figure out exactly what's going wrong here.