Yes but you're replacing a resource with a feature here.
No, I'm replacing an Improvement that happens to be using the art definition for a resource. I've similarly made Features that use art definitions from Improvements (the Monolith in my mod), and I tried a resource that used the graphic of a Feature at one point. My point was that based on the combinations I'd used, the problem seems to be integral to the art definition itself, regardless of what type of entity is using that particular definition at the moment; if the Spices art definition simply has no option for deletion, while all Improvement and Feature definitions do, then it'd explain what I've seen. Of course, it's possible that the problem was purely caused by the fact that I was mixing definition types, so who knows. That's the aggravating part; obviously we can remove resource deposits (since FireTuner lets you do that with a simple right-click in the resource plopper), but doing so through Lua leaves that artifact.
However, I don't believe that the engine is capable of drawing a mine+deer because there is no such art resource.
Correct. I've run into this in my own mod; even if you try modding that XML file, it won't allow new combinations despite the fact that for some resources there doesn't seem to be any combinatoric graphics. (That is, A+B is simply the A graphic with the B graphic laid on top, not A + B + C, where C is something unique to the A+B combo.) I'd wanted to be able to use the uranium graphic for a new water resource that was harvested by an offshore platform, and it just wouldn't work. I ended up having to make an aquatic improvement that used the Mine graphic, which WOULD add correctly to those water-based crystals (although it looks really strange).
In fact, there are no "camp" art files because it is all embedded with deer, elephant and fur art. Mines are different and have unique art when combined with each possible resource.
I've tried spoofing this by having it switch to other combinations (so Uranium + Offshore Platform would use the art definition with the Oil+Offshore combo graphic instead), and it didn't work. I put these attempts on hold for a while, since the game engine has bigger problems with water resources (specifically, that if you add a new water resource the AI will not know how to use a work boat to harvest it), but I've mostly got those straightened out now. So I might try again soon, or at least try to figure out how to create a better combination graphic.
But the way resource art is basically embedded with some improvements (but not others) I have the feeling that you can "trick" the engine into updating resource art. Perhaps. Or not.
The problem with this is that the game seems to use a lot of false entries that its engine knows about but which aren't apparent in the XML. The best examples of this are hills and mountains; they're in the Features file in a "Fake Features" table simply to enable their art definitions, but they're NOT treated as Features by the actual code; Hill and Mountain are, instead, Plot types to allow stacking with other Features. Obviously, the game has no problem placing a forest on a hill, so it looks to me like there's quite a bit of internal overriding being done. I'm not saying that it's not worth trying, but there's just a disturbingly large amount of logic that we don't have access to.
But hey, it's worth a shot. If I had the time I'd try it myself, but I'm going to be pretty busy for the next week or so.