There are already sortof ships like this - have a look at the Enforcer destroyer.
Compared to many destroyers, it's a massive fuel hog - but it does great work!
It might be simpler to make ships like this that have a hyperdrive but it's not a good one. +50% or +100 or even 200% fuel cost compared to usual, burn speeds -1 or -2 or even -3 to usual.
That way, players can use them, move them around, and it explains how they get places that don't have heavy industry (remember it's pretty rare in the vanilla sector to actually have a shipyard!)
It also gives a new consideration above the size of your ships - do you want fuel efficient ships, or not? Currently you only really see this in a couple of ships... only ones I can think of are Enforcer (bad fuel efficiency for a destroyer) and Apogee (Great fuel efficiency for a cruiser)