The reason why Yamato is a BB4 is because, at some point, the BB4s where considered the end-game ships. They then introduced the BB5s and later the BB6s (all fictional) and than EBB2 to EBB6s.
All BB6s are ment to be overdramatized fictional ships. Creatively fun to play and designed to highlight the chosen advantages of the chosen nation (look at Charlemagne). If you want some historic accuracy to the game, just limit rooms to BB4s (nervously looks at H39).
Also, NF doesn't have the resources to get the needed dev support to make any sort of changes like that.