it may be rather difficult to add to the already existing ships without simply creating a surplus of of say cargo or fuel haulers
That is true danger when creating civilian ships. And that is why I think there is eoungh transporters already (ok, maybe frigate transpor ship could be created, but seriously - it is not really needed at all). And that is why I would concentrate on making them (mining and other service providing ships) rather unable to carry too much cargo. That way if You want to play nice (that is peacefully) You would need always a transport ship/ships in addition.
On the subject of civilian ships being converted into the military ships i feel this is a great idea
Well, I like it also
Such assymetric warfare is really interesting - to use "everyday" tools insted of working, to fight an enemy which has regullar weapons. Currently there is no point in that, but when economy will come in... Well... Loos of two, or three civilian ships reffited to fight, and taking down enemy military grade ship in a proces will be propably a good deal economy wise.
So having more of those would be interesting
But all that, as You said, may take place when industrial part of game kick in. Not before. Also we must remember that as civilian ships are being reffited toward military use, oposite situation is alweys an option - imagine mighty Paragon that insted of having guns, have mining blasters