You could go a dwarf fortress route with resources scattered through out various z-levels (When you get to that point) and trade goods to supplement them (Via the shop, or via actual trading with factions), or go a dungeon keeper route with “Nodes” of resources that take significantly longer to hack at but provide an unlimited resource (Gems).
You could also do a “Alchemy/Magic” route where you convert other materials or raw mana into resources…maybe start off with a bad conversion rate (for every 20 cost you get 1 material converted?) that gets better via the tech tree (Down to maybe 3-1 ratio by the end?)
Wood is easy enough, it just…regrow after awhile, or by spells.
The concern for this though would be a “Need” of “Unlimited” resources…I tend to…never need more than what's provided, or even less…maybe a cost to making items/gear (1-3 iron a weapon/gear)…? :-
A thought though…will there ever be a “Food” resource…?
just curious as to if your minions ever get hungry…or why the humans have farms… 🙂