Won't you find yourself at a disadvantage when you will need to build another Capital Ship?
As to answer, this is the wrong question. Better question: won't you find yourself at a disadantage when you don't have an extra frigate factory when enemy is raining corvettes or other such ships down on you?
Greg gave the further reasoning: "You do not need to upgrade planet logistics early on when cash income is lowest."
So, the capital factory is scuttled to make room for other stuff, without costing you the logistics upgrade resources.
For me, I *always* scuttle the capital factory, unless I forget, as happens more often than I would like to admit. In eco slot, I want the 4 logistics slot for a civ research center. In fighting spot, I want the 4 logistics slots for a frigate factory.
If I end up surviving long enough in a competitive game to have enough resources to justify a second capital ship, then I will have enough resources for a new capital ship factory. The location of which will be closer to the front line than my capital planet.