You can leave these slots empty and not put missiles there.I do use them, occasionally, but I wouldn't want them on every ship I build.
Military slots, and I'm amazed this has to be explained again as this is said every time this comes up, are additional slots that were added to military ships. They are a bonus to add to survivability, not a limitation to slots that otherwise could be used for cargo etc. That's like saying you can't put a cargo bay in your armour slot.
As for the military slots, you said the opposite earlier. How nice that on the passenger ships removed the slots for the cabins now you can stuff there reinforcements guards shield.