Although the Tropico Wiki says it otherwise (and does not give any proof for their claim), I've always placed my mines directly on top of the resources (both salt and mineral mines) in Tropico 4 and all the mines eventually depleted all of their reserves. I can't say for sure whether miners work faster if you place the mines next to the resource or right atop of it, but I am certain that it is not true that miners cannot get resources that are right below the mine building.
Check this screenshot below. There was an iron patch in the place of the army base before and there were two mines on top of the patch. So practically most of the iron ore was located directly under the mine buildings but still, that resource got depleted after a few years:
Image is from the sixth extra mission named "Super Hero" (Or "The Masked Avenger" according to the Wiki). You can check the initial state of the island where you can spot the iron patch in this place.
A similar correction for farms: If there are natural trees on top of fertile land and a farm is near, farmers clear the trees and plant their crops. Natural trees don't prevent farmers from working that specific square with the trees. I didn't try this with the trees that are planted by the order of El Presidente.