I have some ideas about sieges. It seems odd to imagine that the samurai could cause enough damage just battering the gate. I could understand if they actually were using siege equipment, but just clanging swords or flinging arrows at the door would do squat. It may be far better to leave things as is for game dynamics, but here's some ideas.

My guess is that most sieges were effectively ended by subterfuge (the only authentic use of battle ninjas), or from simply waiting until the water and food run out. Why not have a food and water gauge that runs out based upon the size of the castle? After a certain length of time the modifiers for the defenders gets so bad that the AI choses to come out from the castle. The current times for waiting out a siege seem ridiculously long.

On the other hand, Osprey publishing discusses siege warfare in Japan, so they did have these devices. The attacker could chose to go ahead and harass the defenders with fire and siege engines. Tossing the dead in could add a whole element of infection, or simply large reductions in morale.

Peace,
Nakamura