deactivation of engine might be cool but you cant be made immovable, every space debrie will still push you around.
As for Capital ships they run on MoX reactors and they need to vent radiation even when not moving, so no engine effect in drydock ok, in middle of space or just in orbit not ok.
As for fliers runing on H-Fuel with engine kill not turning off effect, well it gets reduced to minumum output, it could be speculated that for turning off engine you have to also deactivate H-Fuel reactor and so far every reactor and engine alike takes much more energy to start then to run, which might be also reason why its not turned off.
But for playing on engine failure it would certainly be nice feature.
Zee
P.S. There is surely some switch to turn engine effect off becose when you land on planet it gets deactivated.