If there's room for features like that and smeltmills, dressing plants and the like on the site maybe it needs a new top level catagory so you have 'mines' 'quarries' and 'mineral processing works'.... or somthing a bit less long winded.
I think sparty-lea's idea is most sensible - what about 3 options - Mine/Quarry/Other Features? What other options do you need? It's either a mine, a quarry or a seperate building/feature, it could be on an existing site or not.
So, for example, sparty-lea could create Calder lead works -> Identify it as 'Other features' -> And still label it as 'Lead', adding a brief desciption of the works in the box provided.
MrMike could have Nenthead -> Other features -> Lead (because it/they are still associated with the lead mines!)
I personally like to look at an album containing a mixture of surface & underground. But perhaps when you upload a picture, each picture could be tagged surface/underground to allow sorting if required.
As for adding shafts/trials/tunnels, is that not going to cause problems? When does a trial become a mine? Also, surely a shaft is part of a mine etc.?
Perhaps it would be more sensible for contributers to label each picture they download a bit more specifically regarding the location in the mine, then others can find it using the photograph search already in place on aditnow.