I guess cost, maintenance etc.
Sure, you can build 50 Large freighters and have them go around making stuff (as the human player), but for AI optimization purposes I guess the various sizes are used as the situation dictates (as to how, that is another matter and a question for the developers). From this POV you can also for instance only use Destroyers ever in the game (or switch to Frigates or Capitals once available), but again - due to resource demands, size constraints and maintenance you can mix-and-match...
Military ships division to me is slightly more obvious, due use of different weapon combinations on each of them, i cannot say the same about freighters.
Just, i thought about this more in frame with the smuggling missions, as it is much more effective to use large freighters there.
It's interesting what Erik will tell about this, i'm sure there is a specific reason for this division (at least for private ships).
Once your empire gets larger and you've researched the necessary tech it's quite handy to re-engineer the starting freighter designs so that they can carry more and go further I find.
Yeah, i do the same, it allocates resources much better. I've done 600 size freighters at late game...that's was epic fail however.