Yes. They will probably change this as currently +specific damage type consoles have more benefit than +weapon type. That is unless they expect us to stack multiple damage types at end game, which would be annoying given the paucity of skill points to spend on multiple damage types.
I am currently stacking three +20 phaser consoles.
I have the Automated Defense Turret and two Mark-V Tetryon Pulse Generators stacked with +15 Tetryon weapon damage per console. Will be upgrading them to Mark-VI, soon. Right now, I have about 1,900 DPS on my forward vector when in attack configuration and have Emergency Power to Weapons I, High-Yield Torpedoes I, and Cannon: Rapid-Fire I enabled.
Goes down to about 1,700 when I take the consoles off, and 1,800 when I only take one off.
I got two 3 EPS consoles stacked and you can definitely see the difference when adding the second. I do not think it is a direct linear relationship though because the second one does not improve the power transfer rate as much as the first.