A few mods contain ships that are meant to have a certain weapon in a certain slot -- the Elder Faithopper is 'meant' to have an Ultima in its single large hardpoint, whereas the Nomad Gila Monster is supposed to have the (I can't remember its name right now, some powerful energy weapon the Nomad modder added in), and in the same mod the Yellowjacket "Sniper Frigate" is supposed to have the (horrible underpowered) something-or-other Maser. Of course, you can slot anything else in there, and those weapons can be put in other ships, but you get the idea...