Acceleration and deceleration isn't exactly automated. Your supercruise speed is mostly affected by nearby mass shadows, which interfere with the efficiency of the frame-shift drive. Yes, you do get a bit of assist when approaching less massive objects like stations and USS, but your maximum SC speed is affected by, in order:
your proximity to a star
your proximity to a planet
your proximity to a moon
As you say, you can use a planet's or moon's mass shadow to break when approaching your destination, but its definitely a skill that needs to be practiced. It's also a lot easier with gas giants than it is with rocky bodies, since their mass shadows are a lot bigger, and start affecting you far enough out you can adjust your trajectory for maximum effect.
Personally, I don't adjust my throttle at all in Supercruise. I keep it at 100% all the way. Instead, I use my knowledge of how mass shadows affect supercruise speeds to cut down on travel times. I timed myself when I had stumbled upon an in-system trade route, and on average using mass shadows breaking to arrive at my destination was about 25% faster than the "cruise control" method, despite missing my mark most of the time. Best time was about 33% faster, when I got it almost perfect.
In my opinion, supercruise efficiency is not about what you set your throttle at, but your path through the system as you travel from one place to another. You lose efficiency the longer you stay close to anything but your destination on the way there, and the longer you stay away from your destination primary once you get there. And I've noticed that you get interdicted a lot less, too.