I think the game is set up without rolling effects because of the difficulty this would add to navigating. First off, it's a lot easier to program the AI for enemy ships to use this method, as you aren't having to program in the extra Roll Left and Roll Right maneuvers and making those work with the rest.
I don't think a lot of the usual players would enjoy 3D space, because it would be too disorienting. Some of us would love such a game, because our minds can operate spatially in 3D but I don't think we're the majority.
This is a "maximum playability for all players" call, I believe, regardless of existing limitations in the engine. And I have to say, I do at times feel limited by the inability to fly straight up or straight down, but in almost every instance, it is just as easy to fly down at an angle to the target or target group, then level out and head in.
But this is all just game mechanics. A much more important reason to maintain this system is that this is how Star Trek has always moved and navigated. Vessels in Star Trek almost exclusively behave according to a 2D plane.
There were exceptional times in the series, such as the fleet conflicts at the end of DS9 where a few ships rolled over, or the moment in ST:Insurrection when the Enterprise rolled over and hit the So'na ship on its underbelly, or Admiral Riker flying vertically upwards as it sliced through the Klingon cruiser at the end of TNG's All Good Things... but these are exceptions.
Star Trek was never about realistic 3D axis motion or Newtonian spaceflight. It's about naval vessels on the "sea" of space. And STO should be as well.