Officially? There is no difference.
Unofficially? Smaller ships are expected to be light on guns, but are permitted more freedoms with speed, maneuverability, and specialized functions. Whereas judges expect at least a 'medium' length to fully max out weaponry and expect a ship wishing to push the envelope in shielding, armor, or weaponry to be about as large as a class or ships can be.
Even more unofficially, from a roleplay perspective it is generally understood by avid fleeters and members of staff that larger ships (overall cubic meters of ship) are generally more durable than smaller ships.