Unfortunately adding new options costs time and resources so they need to focus on adding features that have reasonably wide appeal and benefits to most players. Just adding every option that every player asks for will not only mean a huge and unwieldy code base but also waste time that could be more productively spent elsewhere.
This is a feature I doubt many players would want, as it seems a very artificial restriction, your empire should be allowed to have as many ships as it can support and maintain, it's designed around the idea of large fleet combat so the that this is often a fairly large number of ships if you have a large empire and good economy is intended.
You could create a mod for the game yourself that achieves the same thing by making weapons components for ships very, very expensive to build or putting very high maintenance costs on them, ensuring that each ship is an expensive commodity. This will broadly give you what you seek and cost Stardock no wasted resources.
