I am tempted to have something like civilian shipyards, or 'build capacity', or some other 'on-map' capability, but it might turn out to be a lot of work without any major gameplay impact.
If Raiders and NPRs attach and destroy these SYs, these infrastructures do have big impact on a player development/expansion, IMO.
A player could give money, upon request or voluntarily, to commercial lines to help them and rebuid their own yards and ports. Or commercial lines could lend a player (even NPR) civilian yards to rebuild their fleets, until their own infrastructures are out of work.
Maybe software implementation of this can be tricky, but I think gameplay could gain some interesting twist.
About your 5 points:
1. Agree; but you can also consider a fee for moved tonnage/people and/or for moved volume: 1 kilogram is much less than 100 kilograms, and requires less fuel to move it, but 1 kilogram of feathers, straw or cotton wool can be more voluminous than 100 kilos of metal, so requiring a larger ship (in principle)
2. I think of different incremental building costs for the different ship types: e.g. (purely cosmetic, to illustrate the concept!) colony/passengers at N^(3/2) (thanks Nuclear!), freighter/cargo at N*log(N), defence/security/armed ships at N^2 or more, costs that increase even more with the ship tonnage. About these defence ships, I can think about a security branch of a company, with its own defence infrastructures and ships to protect line sites, acting like a sort of a minor NPR
3. Together with the number of ships, also travelled distance can be included (from the start of the shipping line or in the last X months)
4. OK
5. OK (to keep its management simple)
Thank you Steve for your dedication!