Mountains region use special land type 'mountains' for building some of it's buildings.
When resources are depleted and building is demolished 'mountains' area is not returned, instead the amount of empty land is increased. Thus, mountains are finite, and so is the amount of raw resources you can obtain from them, so they are only useful in the early game. Later on, you'd use deep mines, which can be used indefinitely, provided your geologists discovered enough deposits (deep mines use 1 deposit for each 10 units of raw material they'd produce).

'Mountains' can be obtained by either colonizing neutral regions, or sending army on a conquer mission.