Yes all of the cheats still work on Shogun II, atleast in Sengoku Jidai but i assume it works for the others too
Like Cocktopusss said, before going into battle, disable all cheats save for the first two, Undeploy the horses, which basically means the GodMod would correctly go to the men and not the horses, then activate the G Mod and deploy. On the Battle End screen, disable G Mod or disable it when the entire enemy is routed
Same for campaign, althougth the 1 Turn Recruits doesnt work for Navy Units, and the Infinite movement sometimes work for Agents, sometimes doesnt. Didnt try the money mod since its rather easy to get, as for General and Agent points, well those are simple. You just level your general up two times via Normal battle or cheating with God Mod, and then spend the points 1 by 1, reset if necessary. 3 Levels is best since it gives 6 points, which altogether you can use with CE to get 54 points for the rest of the General's skills.
Would've liked if there was a way you could exploit cheat the Unit's XP gain and rank up too but I find that with God Mod, and not auto resolving since GOd mod doesnt affect that, you can simply get rebels all the time and have your units slaughter them to veteran