Of course, the bigger the fuel tanks are the less room thier is for mission-essential stuff. Trading ships that sacrifice cargo for fuel make less money on runs (on thw whole), and militray vessels lose room for weapons, armour and fighters. Its a balance.
Some ships I've designed have had multiple jumps of fuel, but maily raiding and exploratory ships (don't want to get there and not be able to get back).
I don't think it messes with the stellar terrain any, as the ships like that do exist. A 1kdt courier with 2 jump 6s is useful for fast message carrying, but useless in militray or trading roles as it hasn't the room for enough guns/troops/cargo.
Shane