TOW-ships:
may attach to another ship and act as an external booster,
multiple TOW ships may attach to a single craft
That'd be an interesting way to buff fleet speeds, but I think it's too complicated. What we need is for ship travel speed to be separated from battle speeds, so that we can have a passive buff ship that raises the appropriate MutableValue per vessel in the fleet if < X. It'd really, really be nice if fleets were able to be buffed, movement-wise; right now it's like Mount and Blade but without the ability to use your PC's abilities to move a little more rapidly across the map, and players seem to get penalized for fleet sizes much more strongly than the AI is, so I get minor fleets built and they're no longer able to catch anything that they can be expected to kill without fairly major risk (outside of auto-battle, but that's another story).
In Mount and Blade, this issue was handled very nicely in the Warband engine; modders are able to hook their own code into an engine callin and write their own algorithms to determine unit speeds.
Factory-ships:
Capable of converting weapons and/or fuel into supplies
While I don't mind the general idea, the math on that would be pretty important; if you can convert Supplies into weapons, you can build huge numbers of weapons and sell them at a profit, so it needs to be calibrated to require more Supplies than the weapon is worth (which, in most cases, would be about the same amount of cargo space, but not always).
Otherwise, players will just park outside safe bases, buy all the Supplies they can and turn them for a quick profit
Disruptor Ships... Reduce the speed of Fleets you are pursuing on the world map by a set percentage, effect of those ships stack
That sounds like something that would become a major balance issue. Until enemy fleets in a local area can all join a battle, it'd give players a way to pick and choose easy auto-battle wins, amongst other things.