[Will]

Well, I was originally thinking maintainence-free freighters only, but since all hulls are going to cost some amount of organics, eventually you will hit a point where the maintainence on those ships would cause problems. You could make it all maintainence-free, though. Come to think of it, just strategizing for the production and delivery of the freighters would be enough of a hassle without having to think about maintainence and/or supply issues.

Modification then: three kinds of spaceyard facilities.
1. Spaceport, same as before; constructs at 3000/100/3000 (might want to tweak those values to account for population bonuses). Produces 2000 organics/turn, stores 2000 organics. Scraps at 110% efficiency, and can resupply. Costs 100k organics to build.
2. Launch Pad, same as before; constructs at 0/2000/0, produces 2000 organics/turn, stores 2000 organics. Costs almost nothing to build (1 organic?), it's assumed that the colony ship already has the materials, and it only requires a bit of work to set it up. Upgrades to Spaceport.
3. Military Base; constructs at 1500/50/1500, produces 50 organics/turn, stores 250. Can resupply ships, and provides extra unit spaces. Maybe higher tech gives ship/fleet training. Costs 20k organics to build, maybe more at higher tech. Possibly would also upgrade to Spaceport (or a derivative, Military Spaceport, with the training, unit spaces, etc included).