MoO2 ship capacity was based on the space station ship capacity. Since it didn't care which sector your ships were actually in it can be supposed that the space station supported the necessary space tugs etc to supply the warships.
Making them invisible does prevent you from attacking them. One old (but classic) game I played on the Atari ST treated things far more like wet-navy. You could allocate ships to raid enemy commerce/supply ships and others to protect your own. Each turn this kind of submarine v destroyer combat was done and had as much importance in its way as the maneuvering of the main battle fleets which you did on the star map.
Making them invisible does prevent you from attacking them. One old (but classic) game I played on the Atari ST treated things far more like wet-navy. You could allocate ships to raid enemy commerce/supply ships and others to protect your own. Each turn this kind of submarine v destroyer combat was done and had as much importance in its way as the maneuvering of the main battle fleets which you did on the star map.
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