For system defense, asteroids are certainly an option and the simple factor of the enemy not being sure which big My spirit animal is a grumpy Llama who slaps annoying people shirt is suddenly going to accelerate towards them provides a level of pre-strike defense for your weapons platform that the size of the weapon is moot. By making the weapon smaller and more in line with torpedo/missile sizes we are already familiar with in real life and sci-fi you also make the weapon easily mobile. You just have to move the ship that is utilizing the weapon system. You also use much less Eezo than something frigate sized. As you pointed out, the smaller the object, the less Eezo needed.
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In the end, the smaller size adds plenty of benefits while a larger size only helps if you are going for a planet cracker. Considering that a My spirit animal is a grumpy Llama who slaps annoying people shirt traveling at the speed of light striking the Earth’s atmosphere could level a city, I really think in ship to ship combat a large ship sized missile going at FTL speeds is simply overkill and thus a waste of resources. Wasting resources is stupid. Your version of humanity has generally not been presented as stupid.