What if there is only scent but the scent along with some strength score would also have a source ID and when scent spreads it just uses whichever source is stronger. The downside of course is that you can't have a scent of rotten meat under which you catch a slight wiff of plant matter.
Yea this is more or less what I was thinking, but it means that you have to accumulate the strengths of the surrounding tiles in the diffusion step and then decide which one is strongest instead of just summing them, and this happens in an inner-inner loop that's frequently a bottleneck for the game. This is nowhere near as bad as having multiple independent scentmaps, and I'm not sure how valuable being able to smell multiple scents would be, or if its even reasonable to give that ability to unaugmented humans. We can and do have bionics and muations for enhancing scent sensitivity, but then it's a question of slowing the entire game down in order to support optional abilities.
Also problematic is that this bottleneck would be enlarged multiplicatively by the merged z-level feature since we'd want to start diffusing in 3D. So keeping an eye out for that as well.
Your right, scent would cause a big problem in 3D. One way I could see of keeping this down is to not keep track of it tile by tile but rather have an area where it is tracked in like how Minecraft has chunks. This would reduce the granularity of the system though depending on how big an area each "chunk" is you would be reducing the number of calculations by quite a bit. The only problem I can see now that I think about it is that besides some of the far roaming stuff which appears away from its source area anything of interest you would be able to smell you can also see on the map. What good is smelling gasoline if you already have the station on the map. The only point of it at that point would be tracking specific types of zombies and that would need a tile by tile diffusion and thus we are back to square one. The more I think about the problems and what it would provide all I can see is that you would need to seriously nerf how the automap works to make smells useful for map features like a gas station. I actually have rewritten this post a number of times with a few different ways of working with the tile by tile and section by section method but in the end I think it might be better to just drop it. The benefits would not provide something worthwhile for the cost in performance and the best way I found to get around that would not be worth it because of the characters sight radius and apparent x-ray vision when it comes to mapping.
Any traits that let you have better sense of smell should instead work like the infrared vision but instead of showing exactly where stuff is with a red ? it shows where any creature with a scent is and represents them with a symbol depending on what they smell like, most zombies could be a z with the normal zombie color, a few specials might be identifiable by scent and thus have their own colors though skeletons should not show up, carnivore animals could be something like a red C, herbivores could be an h of some color, the fungus and triffids could be a 'p' of some sort and better levels of being able to smell would give the fungoids a red f maybe, strange creatures you would not have experienced could be red ! so stuff like the Cthulhu stuff, and if you had a strong enough sense of smell things like the burrowing wurms and graboids may show up. It could also be in a somewhat random place like how the noise markers are and if you manage to get both inf vision and the smelling trait it pinpoints where with the symbol. Robots and such of course should never show up along with some other things.