You're thinking from a gamer's point of view though. Not a designer.
Why were anti-tank guns and tank destroyers even used during WW2? They were far less agile since they had no moving turret, and could very easily be blindsided by turreted tanks. They also typically carried no anti-infantry defenses, so were especially vulnerable to infantry attacks too. But they were built en masse. Why? Because of costs. A turret required a power-train and the systems to move the heavy turret, thus taking up precious internal space and adding significant mass to a vehicle (thus slowing it down). A turret, like any moving system, also demands far more maintenance and much more complexity of repair than something as simple as a cannon barrel. It is also generally weaker since it's base has to be movable rather than fixed, so the seal may be exploited for this purpose. Also, the armor due to the hole that has to be cut for firing mechanisms to go up into the turret, and it's likely the turret won't be wearing armor plating as thick as the hull so will in itself be a vehicle vulnerability.
Of course this isn't fair when in comparison to starships, but my point still stands -- sticking as much firepower and equipment on a vessel as possible isn't always the best strategic solution. This vessel may actually operate with teamwork rather than attempting to be a one-ship fortress. The vessel may be intended as a high-speed raider, and has the minimum viable amount of equipment as to maximize it's speed and whatnot much like how tank destroyers usually gave up armor, versatility, and infantry defenses to provide a high-speed, high-damage tank killer.
On that note I'd point out that the reasons may not be purely IC. Yamatai, like most nations, has been generally downgrading its technology so as to avoid powergaming (i.e., my ship annihilates your entire fleet! Ha-ha!). Having a vessel that doesn't have complete coverage may also encourage inter-ship teamwork during fleet operations more than ever before.