Having multiples of the same weapon doesn't have any effect on damage, durability, etc. The second weapon is completely extraneous except for under one specific circumstance. If you get heavily damaged (as in only 10% of your total energy remaining) then there's a chance your active weapon will be destroyed. In such a case having a second of your active weapon can keep you in fighting shape as if nothing had happened, although I'm personally of the opinion that if you're getting that close to death then the cost of the second weapon would have been much better spent on an extra Phase Shield or two.