In another post, I talked about my experience with 0.6a and why I felt it was better than its predecessors. To summarize, it added depth because it added meaningful player choices and considerations with the introduction of CR.
But another important aspect of games like starsector for me is character progression. To a certain extent we already have that with player skills, but for me I'm talking specifically about ship improvements. Eventually we are sure to see other ways of making credits outside of combat. But what I am not seeing right now are many ways to
improve your current ship. That's not to say there aren't plenty of play style customization options (torpedoes vs LR missles for instance), and some weapons are arguably
better in their role than others and could technically be called an upgrade, but there just is not much to actually spend your credits on other than more ships or supplies.
So, in the interests of those who prefer smaller fleets that prioritize powerful flagships, more ways are needed to improve said flagship other than skills in Combat. In other words, definitive "gear" progression similar to RPGs of one ship based on more weapon quality tiers (already possible through modding) and other ways to spend money improving said ship.
That is why having hullmods cost credits to fit (so you "buy" hullmods at a station after they become unlocked through skills) as well as OP would add meaningful gameplay progression. It gives the player something to work towards and gives more choices on what to spend their money on to directly improve their ship's capabilities.
Having missiles cost credits to replace also indirectly improves a ship, but I am less enamored of this one since it is a little too logistic-y and we already have a pretty decent logistics system.
Either way, it also helps facilitate a reason to travel and explore within the game universe. Different stations offer different quality weapons, missile types and hullmod options. Higher tier is more expensive, less accessible or hidden. This also allows for faction specific improvements to increase variety and flavor.
For those who would rather rely on "more is better" and focus on larger fleet logistics and management, it does not limit much. Many ships with weaker weapons or no hull mods would perform roughly the same cost for cost as a couple ships with a lot of money invested into their improvement. In terms of loss, larger fleet's losses are easier to replace but happen more frequently while an elite ship's loss is a severe blow to the player's wallet but less likely to happen due to overall ship quality.
The point is that it not only creates variety and a more concise play style option, it gives the player more to do, more to gain, and more to enjoy.