It's almost mandatory to leave some slots open on a lot of ships, especially if you're trying to get some focused firepower. I run Atlas mkII with two locusts, two mjolnirs and two machine guns on the front to stop a few missiles. No side guns because it's not for charging into formations anyway. This leaves a lot of extra points for flux control and maneuvering mods. Salamanders MIGHT hit my engines if I'm not paying attention, but that's what omni shields are for.
Now on AI ships it makes sense to run lots of point defense efficient weapons and survival upgrades, since the AI just can't seem to handle nuanced combat anyway. This lets the AI tank damage longer while you get the job done and it'll maybe take out a few frigates and destroyers along the way.
