one question for the development team and im sure this is in the wrong place did anyone else think that when a ship is stopped the engines shouldn't be lit.
IIRC it has been thought, but most likely it's being kept as is to retain the FreeSpace 2 feel on that part. If the game was more simulator and less arcade, it would be more likely to be dealt with, but as it is... I prefer to think it like this:
When you drive a car, even when the engine is idling it makes some sound. Completely shutting off your engine while driving isn't really a good idea because it powers the electrics, brakes (to varying extent), power steering and then some. Also, re-starting the engine on the fly takes some time and attention. Similarly I would think that when the engines in FS2 are on idle, they still need some fuel to keep them running. Who knows what kind of an ordeal it is to actually fire up those engines - you most likely don't just throttle them up. There's probably multiple pages long checklists for operating them...
and am i the only one that has the engine glow bleed through the ship models
You're not the only one, and it's highly model specific. Some have their thruster points set so that very little or no clipping at all occurs, some have been designed with older POF thrusters in mind and thus can have more problems with animated thruster effects, especially if the thrusters are recessed in the hull (like in case of GTF Apollo).
I don't know what can be done about it, though, apart from making separate thruster glow animations for different ships so that clipping doesn't occur even at full thrust. That would take a lot of time and effort and would also require changes to ship tables so that the ships would actually use their specific thruster effect.
Quite possible the long rumoured and anticipated shaders could be better for utilizing light effects like this, but that's a long way into the future I think, and won't be any kind of holy grail in itself...