The ironic thing is that right now, beam arrays and dual beam banks are the weapons that deals the most damage, not Dual Heavy Cannons.
Its gotten to the point that both my science officer's Recluse and engineer's Galor is not only out-damaging my tactical officer's Fleet Armitage, they also out-tank, out-heal and out-science my tac's Fleet Armitage. Especially my Recluse, everyone wants it in their STF runs because this one ship alone is capable of debuffing all nearby enemy ships with 5xAP:Beta III and 1xAP:Beta II. Typically, everyone sees a +3-4k dps boost just by having my Recluse in the team.
And then the parsers only take into account actually dealt damage.
They don't measure the raw output I think which can be diminished significantly by resists and defenses.
Actually, the latest ACT plugins for STO keep track of both base damage and actual damage. So they also give two dps figures, theoretical dps and actual dps.