The Yamato was sunk by bombs from small aircraft and torpedoes (that can be launched by small ships). All it's anti aircraft and point defence weapons were overwhelmed by the numbers of targets. Independently targeting many guns most efficiently is not easy. However, as you said, there is no phase shift in space like air and water.
A way to add the phase shift back is to add stealth, so that smaller ships can load up huge bomb/torpedo type things, stealth into range , fire and run away. The (obviously fictional) stealth mechanic would be such that the power required increases exponentially based on ship volume.
Then you could have stealth breaking sensors that require exponential power for range so they are best used on multiple small craft to cover larger areas.
If bigger is always better, then without severe resource restrictions, it makes combat dull, time consuming or to be avoided, as the limitation on the biggest ships (availability) doesn't exist with virtually infinite resources.