Ok, so it looks like it IS working...i can see my faction coin totals increasing, just kinda threw me off since i couldn't see anything, or hear anything that would indicate some passive clicking process initially.
So i purchased the farming assistant upgrade after i got 100 farms, and it doesn't seem to be working. There is no indication that i can see of any passive chest clicking going on.
 "Realm Grinder"){kind=icon}
After unlocking a Clicking Assistant, a new line will appear in the Stats tab telling you how many coins per second they are producing.