(I still refer to them as torps out of habit. Maybe we'll change the name if I can't force myself to change...)
But yeah, Missiles have numerous different payload types, which constitute the main weaponry. EMP and Explosive are the two main ones, but I am thinking of adding a more nasty EMP-style weapon which also resets any systems which aren't hardened against them.
CIWS will exist for taking out missiles, but are not designed for going at other ships.
However, I am working on mines. Of course, these are more 'mines' in the sense of very tricksy programmable missiles, rather than static objects that just blow up when you get close.
The mechanics (which mostly work) would be something like: fire your mines into a region, pre-programmed with a radius and even certain details of what kind of sensor hits will activate them, and then when they activate they become missiles, as normal.
The theory being you can use all kinds of tricks to either get an enemy to head toward a mine field, or better still, use a mine field to make an enemy think you're in entirely the wrong location.