Nuke

Nuke (also known as Capital Missle) is special module type that can be put into Nuke slots. Unique among modules, nukes are used one-time only, after which you have to use another nuke, crafting ship-specific one in slot or finding one in the shop. Relatively large nuke cost compared to other weapons is compensated by their potential high damage that can swing victory to your side

Nukes proper usage
When in battle, you can select any nukes you have in F5 quick selection menu near other weapons and then order them fo be fired at any point of any ship. Nukes don't require energy or bridge, start flyinng upon commanded with minimal delay and are fairly accurate. Immediately after nuke slot goes empty, you can select it and craft another nuke, which you can also send.

As nukes cost fairly high, it is best to use them when tactically advisable. Nuking junk pile of third-rate pirate is not a best choice when you can just obliterate the trash without harm for yourself, but when you are attacked by multiple strong ships nuking one to stop it firing might mean difference between taking fatal damage or not.

Be wary that nukes can be destroyed by point defences. Thus, for maximum effectiveness you should play around that: use multiple nukes (or other weapons that are targetable by point defences) at once, use better armored nukes, take down point defences with other weapons or just aim at parts of the ship that are not covered by point defences. Ideally one of escord ships doesn't have point defences at all, which allows you to concentrate fire on other ships.