Speaking as one with some programming experience, the work on new ships would mostly be done by artist types, not programmer types. A few exceptions would be unique consoles that require supporting code, possibly minor UI changes to accommodate a larger then normal number of weapon slots, and possibly ship interior connections. (Exactly how much code is needed, and if some of those actually need code changes, would depend on how good their dev tools are.)

Debugging a program as complex as this is cannot be easy, and if the programmers can't get a particular bug to occur for them, they might not be able to fix it. System configurations in the PC world vary so much that there could be bugs that only affect one out of a million people. Both software and hardware can interact with a program in unexpected ways. (And by software I mean any programs running on a particular computer, not just drivers, and including stuff you may not even realize is running.)