Got to echo Sterl here, editing vanilla behavior is generally bad idea. That's not to say you shouldn't but if you do tread very carefully.
I modified a vanilla Atlas, it carried over to EVERY Atlas in the modiverse. Bad idea.
I also modified the Mining Laser to become a hybrid and somehow that ended up becoming part of the base game, occasionally you get lucky... it's far more likely you won't.
That's not to say I won't help you cause chaos
There's two ways to go about it:
You could clone a copy of each missiles file in to your mod (same file path) then in your mod_info.json specify to
replace those specific files. If you want to see this in action check out my
Koc. I did it with some .econ files. It's a brute force method but it works, in my case I resorted to this because, by default, Starsector tries to merge files and doing so resulted in unexpected behavior. I've just got to be mindful that if Alex ever makes changes to those vanilla files I have to update mine accordingly.
Alternatively:
If you create a .wpn file for each missile in your mod you can remove
all render hints for that missile with the following snippet of code.
Again, take a look at my
Koc, I used a similar method with phasebeam.wpn to add(/merge) a script that makes the vanilla phase beam deal hardflux to shields on certain ships.