IMO it's a mostly unnecessary step to actually have to research the engines unless you can re-use the missile engine for other design and purposes like miniature fighters, drones or shuttles for boarding assaults. The extra cost of research for missile engines is also so minor that I don't think it really matters in the long run.
Taking away the fuel efficiency choice and making it automatically the best is a no-brainier unless you want to attach it to a higher unit cost ( retain ability to build older inefficient but cheaper engines for the missiles )
But as you say it comes down a bit to play-style too. For a player really doing micromanagement with 10-20 different missile designs in use at the same time I can totally see a point in keeping the engine design step and retaining the choice of how many engines you need to design just like when you have this amount of ship designs.
But for most players I think you stick with 2-3 designs that have pretty different engine needs anyways ( AMM, Fast shortrange ASM and Slow longrange ASM ), and then engine research is an extra step only gets in the way except for some minor flavor addition.
We can make missile engines nothing more than another MSP slider in missile design. Would that be oversimplification? Would you lose some sort of gameplay value? Or does it add to the overall usability and user experience?
Yes that would be oversimplification IMO since it's very important for gameplay to be able to specify power mod to differentiate between efficient slow or ineffective fast missiles.
It would also be nice to keep the ability to design missile buses that release multiple other missiles ( not really related to missile engine design perhaps, but still something to keep in mind when designing the interface/gameplay ).
Suggestion ( Depending on how much you want/can deviate from base Aurora experience ):
What would be pretty cool is having a few things to choose from anyways except for the normal missile engine choices, for example what if you had a few engine manufacturers in your empire to choose from for all engine designs that can tweak the stats around a bit to make it more interesting. This is on top of the normal choices of power-mod and size.
Example:
Manufacturer X (missile) engines gain +10% higher Powermod but will consume 5% more fuel
Manufacturer Y (missile) engines have -5% less fuel consumption but will add 10% higher research cost/time for the missile
That way you can retain the flavor and choice part, while keeping the interface simple only adding an extra drop-down ( instead of fuel efficiency choice perhaps? )