Either no weapons in mounts or even putting smaller weapons in oversized mounts.
Lately, while trying to make Onslaught better enough at surviving and killing things in endgame fights, I started to remove luxuries like Vulcans on small mounts, and downsizing a heavy to Heavy Needler because it was more efficient than the heavy weapons. Later, I started doing likewise for other ships, trying to keep them close to flux neutral. Conquest only gets three ballistics out of four per side. (800 range in the rearmost turret is not very helpful if ship fires most at 900 range, and I need more OP for Expanded Missile Racks to power Locusts). Legion has the majority of its mounts empty. Only two heavy weapons, two dual flak, and maybe a heavy needler. Partly to keep flux use under control and partly to have enough OP to get more important stats.
Special mention and worst offender is Odyssey. Two plasma cannons, some beam PD (seven burst PD or twelve normal PD), Xyphos and Longbow fighters. Everything else in vents and hullmods. Like the three lance Odyssey from 0.8.1a, two plasma Odyssey with tons of dissipation and little else is highly effective as a playership. With enough combat skills, it is probably among the top two capital-sized brawlers. Only Paragon might be better than it. It looks stupid with only two significant guns, all on the left, and most mounts empty, but it is bizarrely effective. As for AI using it, forget it. It burns in like stupid and dies.
It seems filling in all mounts is mostly for cheap (or undersized) weapons with low OP and flux costs. When player wants to use elite weapons, mounts probably need to be left empty. Starsector is not the only game that works like this; those who play Endless Sky probably do something similar. Use lots of blasters or other cheap weapons, or fewer electron beams, particle cannons, or expensive alien stuff.
P.S. I was wrong about worst offender. That goes to Drover. All of them I use are completely unarmed, and rely totally on fighters for combat.