I thought we were able to do something with the economy, and sabotage businesses such as mills and stuff... All the shopkeepers seem to restock their items and coins magically. Where is it in the game? How do I affect it?

Have you tried killing farmers in the hold?

It does seem to be a lot easier to improve the local economy than it is to destroy it.

Well I've noticed the shopkeepers tend to have icrementally more money in a hold where you've helped out a lot of people. There are global variables that track favors done in various holds (well beyond and outside of what is used for the Thane quests) and most shopkeepers within that hold appear to get a bonus to their gold proportional to that. For example, I have done every non-repeatable quest in Solitude and even the outdoor food merchans have almost 2000 gold and one of the merchants (either fletcher or blacksmith) has around 4400.

I do have the investor and master merchant perks on this play-through (a waste in terms of most gameplay aspects I know) but with them and before doing quests there all merchants had about 800-1200 less gold each and this increase appeared to affect merchants who did not have the invest option and did not appear to be affected by master merchant. Additionally, at my current level, it does appear (this may be mistaken perception on my part) that these merchants have far better selections and stock compared to holds where I have not done any quests.

As far as damaging the economy goes, I'll check through the global variables lists for hold-name and see if any of them might be relevent. Then I'll see what I can do in normal gameplay which might change them and see if it has this effect. Worse comes to worse I'll murder some mill and mine owners and works and maybe a few farmers and see if that helps hurt the economy.

I was under the impression that it dosent have an economy but just an random generator adjusted by perks, skills and level.

In each shop you can find the business ledger (whiterun, blacksmith one is upstairs on the draws.) walking up to it gives you the option to Forge numbers, never works for me though, keeps saying nothing to change, guess I'm missing something.

The business ledger is for some thieves guild quests.