so effectively the duration stacks but not the effect?
The effects originally did stack, but after many complaints about broiled Federation ships in Romulan space, (and it was so bad that 'Hazard Emitters' was a required skill for that region...) it was changed to the current state that it is today...
If you haven't experienced it yet, a High Yield Plasma Torpedo plasma fire will tic damage in the 3 digit range. A D'deridex Battleship will launch 3 HYTs are special attack. So 3HYT from a boss and 3x3-digit DoT afterwards if you survived the initial impact. Not good.
take a look at the proc description on your energy plasma weapons, they don't leave a DOT anymore, they just have a chance to deal extra damage. torpedoes im not sure how many DOT's stack, proboly doesn't mater because torps don't exactly hive a high rate of fire.