Weapon types do get different bonuses. Katana gets a strong anti-infantry bonus. Yari get a strong anti-cavalry bonus. Naginata gets a mild anti-infantry and a mild anti-cavalry bonus. Thus, as specialised killers yari and katana units are superior, whereas naginata are capable of performing well all-round. If the game didn't set bonuses in this fashion, naginata units would render the rest obsolete.

Naginata warrior monks are set up as shock troops. Katana are designed to kill steadily, and they get a bonus versus the monks. Wave versus rock; if the wave cannot drown the rock swiftly, the rock will outlast it.