They still take up space and you no longer get free maintenance from unlimited maintenance stations if you are under a certain size. This means that having lots of relatively large but cheap PD will be heavy on your maintenance infrastructure.
Except that isn't really a concern because railgun stations are so cheap that you can easily afford to give them 20+ years of maintenance life and just scrap them when the time runs out. As it stands, railguns are hilariously good at beam point-defence and dominate over the other options available at low tech level. Even worse, the lowest tech railguns are the most effective, and better tech doesn't really do anything for railgun PD.
One problem here also is that your stations will put strain on the maintenance location even if they have extreme long life or you will have to place them away from that maintenance point which will be a problem unless you are at a fixed point in space... at least it is irritating micromanagement.
It also is against the spirit of the game so you probably should just NOT do it. There are many mechanics in the game that can be GAMED... this is primarily a single player game where you can do whatever you feel is OK.
If you want to go against the spirit of the games mechanics just to get a benefit I don't think Aurora is a good game, there are quite a few loopholes and ways to sort of Game the system.
One of the main problem I have with cost of resources is primarily a gaming issue. Games tend to make more advance technology cost more in resources while in reality this rarely is the case. The cost are generally in development and prototyping, once something are put in to large scale production cost always goes down to roughly the same values as older similar technologies. Sure, high tech equipment tend to make things more expensive and complicated but that is more in man ours and logistical costs, but in time even those things tend to go down in costs. In general a tank 50 years ago was as expensive as a similar tank today to actually produce after say 500 were built.
There also are a reason why there is a very strong focus today on modularity in almost all modern military platforms.
I wish games simulated this better where it is the research and development that is costly but an old ship are still going to cost almost as much to build in terms of resources as a new one.