It's a limitation of the display convention: a space consists out of two elements (the space itself and a floor), but there can be only one on the display. In the current game Sowelu's solution would be non-disruptive, but convey the extra information for those who wish to know it, respecting the logic that dwarves mine out an entire space except the floor. It should be displayed in the messages as eg. "You have struck emerald!", however, if dig underneath an emerald square.
(Aside: Which reminds me that changing the occurrence of gems so that we have "Bauxite, containing sapphires" rather than a complete square of sapphire would be nice and more interesting to display (background colour would be that of the stone, foreground color of the gem itself). Although that should be possible, but it's a huge quantity, a gem or gem cluster you can make a statue out of should be a non-artifact artifact level rarity.
Alternatively, any bauxite square could have a % chance (varying with locality, so you still have sapphire-rich and sapphire-poor areas) to yield a few sapphires when mined out, but you wouldn't be able to notice it beforehand that it contained sapphires, only deducing it from the previous yields of the local bauxite would work.)
Taking the other route would also be possible, and that's assuming a wall and ceiling in every square like there is a floor now. That would reveal only the rock of the square itself. It becomes possible to make thin walls that way (very useful for cabins, tents, tree houses, glass panes, etc.), but it would mean a definitive farewell to the ASCII-style display. It also means potentially more complicated commands, with all the beneficial and detrimental issues that brings.