They accelerate to the midway point of a route, and decel afterwards.
As a pedant, I feel compelled to correct you here: they decelerate in order to stop on the planet. For long journeys, that may be weeks after the midway point. This is because maximum speed is 5.0 units a turn, so it's quite easy to reach that for some ships.
After a little bit of playing, you can usually take a decent guess about how long it'll take to reach somewhere with different fleets.
