I agree with the missiles being difficult to see. Their trails are barely visible puffs of white smoke, but the issue is purely cosmetic. There are several mods that have redone effects that you might want to look at. I personally use Bailknight's Graphic Mod (
https://forums.sinsofasolarempire.com/301418), but there are several others out there that you might be interested in. Just look at the Modding sub-forum.
EDIT: Because of the recent 1.04 patch some mods may not work. If you're still on 1.03 you can see what the current mod releases can do, but you may have to wait a bit before they're compatible with 1.04.