mainly because the main drive is too wimpy to carry enough fuel to be used to decelerate as well and is worthless without fuel. Carrying a refinery to generate fuel on destination is too heavy and unreliable as well as we aren't talking of simple dumb hydrogen but deutherium or helium-3 (complex machinery won't last so much time as the voyage anyway so).
Btw, it's not that fusion is "wimpy" it's that interstellar voyages require mindboggingly ridicolous amounts of power even for a fly-by of the closest star in our neighbourhood (like say Project Daedalus). So yeah. Either that or we sit here forever.
Well I wasn't thinking no-return trip when I posted that.
Obviously using the drive to decelerate is inefficient, better to use magnetic sails for entering a system and aerobraking/aerocapture for entering orbit whenever possible.
It's more like using the all the fuel you can possibly carry in the acceleration phase allows to have the shortest possible travel times. Depending on how good magsails (or electrostatic sails) turn out to be, they may or may not be a good idea to decelerate. For now it's too early to know. (as for fusion engines for that matter)