Supplies, or a lack there of could reduce maximum defense and/or health. I am not sure I'd affect attack, unless they were missile troops. How you would track supplies lines I am not sure. You could create a unit, similar to the caravan, but call it a supply train or some thing, and move it to the unit. The supply train creates a small, "stock," or materials the army uses when it travels. Unless the army is equipped with Pioneer gear, or maybe some thing like Ranger Gear, its maintenance cost in materials goes against this small, accumulated resource, for that particular army. Only reduce the stock pile if the army is out of your ZOC. This would also put most of the exploration to adventurers and the sovereign since they would need the supply train. You could even create of mod present Traits to support this idea.
As for defenses, I've been wondering if they couldn't do more of a AoW thing. Don't draw the whole town for the map. Instead, I'd do piece-meal maps. Create wall sections for each type of defense. One for palisades, one for basic stone, with square towers, and one for thick walls, with round towers. Just use elevated terrain with the walls that can't be passed through. More like a cliff maybe, with the wall as the cliff. Make all walls a square wide so troops can move along them. and just use a ramp to access them or wide stairs simulating a ramp. The tricky part would be the gate. I don't know if there are any spells present that could simulate a gate, but maybe use that to make a pretend gate. Maybe even as a summoned, "creature," that can't move or attack. It just as HP's and armor. As long as it looks and acts like a gate, you should be good to go.
As for wall simulated defense, use the terrain modifieres, except add a dodge bonus instead of armor. If an arrow can hit you, it should hit you for full effect. Dump the extra HP's that the supposed defenses give now. Also, as I think of it, if it's possible. treat the wall part of the terrain as a critter or destructable object. If it's destroyed, it collapses into a, "ramp of rubble." Can they deform terrain in battles? Catapults could actually have a use besides acting as an archer unit that fires sabot rounds. Some things off the top of my head.