I assume DFHack has access to the "hidden" flag for tiles? I don't recall if Visual Fortress uses DFHack, but I know it has functionality to not show hidden tiles. In any case, it's a pretty simple thing to add if you know where it's stored in memory. Although it does leave a hanging question about implementation: what goes in the blank spaces?
I suggest we follow DF's own route and have simple black squares. In terms of memory usage, a single bit colour depth is the best you can get pretty much, and you would only have to store one square in total.
A number of questions on implementation (I guess I could search the source for myself and find out, but anyway - feel free to ignore the wall of text): what level of caching does Stonesense use? As I see it, you can either cache all images necessary to render the displayed area of the fortress, or you can cache the images for the entire fortress - the latter has a bigger memory footprint but makes switching between levels and scrolling around faster. Does Stonesense cache only the images it needs, or does it cache (say) all the images relating to a certain material? Are all displayed tiles cached, or only those that recur many times in the one display? What about tiles that are within the area to be displayed but occluded by other tiles?
Now it's probably too much to ask, but would it be possible in the future to force Stonesense to use a specific level of caching? So if somebody had severe memory constraints or, conversely, an overabundance of memory, they could instruct Stonesense to cache more or fewer images? Obviously not important right now, but perhaps something to think about.