The textures are based on .dds files and .asset scripts in Stellaris > gfx > particles > combat and Stellaris > gfx > particles
use paint.net to edit the .dds files and notepad++ to edit the .asset scripts
As far I as I know saving them using the method A8 something works to keep the same amount of quality correct me if I am wrong.
Now, this bit is complicated.
The effect has the description, this is defined into a "pdxparticle" file in Stellaris > gfx > particles > xxx.gfx
The .gfx file is editable using notepad++
Then the whole thing is defined into a projectile graphics entity in Stellaris > gfx > models > combat_items > yyy.asset
the entities are then grouped up into the name that the weapon template uses, such as "mass_driver_s" in Stellaris > gfx > projectiles > aaa.txt
ie missiles.txt
the weapon templates that define the weapons are found in Stellaris > common > component_templates
I recommend you study the code and mess around with it to figure it out.
Hope this helps and somebody sticks it on the wiki.
Further if you want to edit the game files and make a mod I recommend backing up your mod files incase you mess something up or create a mod using the mod tools in the Stellaris launcher.