If this is theoretically real in-game having both slots as swords would make the wakzashi look the same as the mainhand katana unless you resize it, hence the dagger slot.
A wakizashi’s in-between the size of a gladius and the combat knife to begin with, and mostly only used to cut your own guts. It’s considered a short sword still, but if this is ever ingame having 2 swords wouldn’t make the offhand a wakizashi.
Also, Samurai’s better off in the archer tree. Before Tokugawa novelized them to be these flawless swordsmen they were expert bowmen and spear-users. It could have been like Survival/Melee Hunter in WoW (at least, Legion is bringing melee hunter back) using polearms and bows. Nobunaga’s loyalists were no foreigner to muskets too.