Tough call... ridiculously powerful engines will get you where want to go quicker, and orbital maneuvers will likely be quicker, but I think you will lose some fine control (using the on-screen controls, or mousewheel, best you can do is 1% increments — not sure if an external throttle will give you that fine control). That fine control may be the difference between flying off into space or crashing into the ground when flying in-atmosphere. Only you can decide that.
You could try using a starship with the fast hyperdrive you like, and add a dock to it (if it doesn't already have one). Dock a planetship or shuttle that has the attributes better suited for in-atmosphere flight to that dock. That way you also get to practice orbital maneuvers, rendezvous, and docking.