An alternative to letting a mine collapse because of nothing to mine would be to destroy the mine when it starts it's last cycle. Some of the resources used to build the mine will be returned.
It took me a number of levels to realize this, but you do not need to run mines continuously all the time. If you have a store of ore or bars that is growing rather than holding steady or decreasing, turn off the mines or leave a deposit untouched.
Don't operate a gold mine, or for that matter a gold smelter and coinage, unless they are buffed with at least a basket. I've even played with letting coal and iron mines go idle unless buffed.
The only deposit I'll think about spending gems for it the Golden Parrot. As far as deposits on the TO, compare the price of the deposit with the price of the same amount of ore and bars. Be smart how you spend your hard earned coin.
I like the idea of building one mine to level 5, leaving it idle unless buffed, and dropping deposits found on adventures into it. I can see doing that for gold, coal, and iron.