It just makes good sense, and adds more "story" elements for the game. Yeah you've got your big honking T9 cow, or Clipper, or Anaconda, but maybe you've been asked to take some secret plans to a distant outpost. Only you can't.
Some of us don't want to swap ships all the time, our ship becomes our home. Therefore the more versatile the ship can be, the more fun we can have with it.
It certainly wouldn't be game breaking in any way. You couldn't easily trade large amounts of anything with a station. Hell, if it's a Condor or an Imp fighter, you might not be able to carry anything. But you could still take on kill contracts or ferry messages.