There are too many things that can be pointed at as "realistic" reasons why a ship can or cannot do this or that thing. Lower agility might make sense due to the size, but speed not necessarily. If we're looking for balance and a spread of ships being used in the game, then creative license like "yeah she's big but she's all engines and power plant so she's fast" is necessary.
I really want to see noticable differences from class to class and ship to ship. I'm fully in support of making Liners more interesting than their current incarnations. Does that mean more speed than other transports? Better guns? Both? Something else? In any case, if they become more unique by means that make them more capable in combat then they need to lose significant cargo space.
"To gain a hundred victories in a hundred battles is not the highest excellence;
to subjugate the enemy's army without doing battle is the highest of excellence."