So we have a contaminant system which is effective at distributing dysentery and similar maladies. We have a selection of materials which can be either good or bad from the perspective of real-life sanitation, but this does not interact with the contaminant system. I propose this be rectified.
For example, lead is well-known to introduce contamination that can cause long-term health effects when it builds up in a body. Lead was also popular as a pipe due to its ease of accessibility and ease of manufacture. This can unfortunately cause a lot of issues. So I think that lead ought to contaminate things it is used to hold. For example, lead pipes in screw pumps would introduce a contaminant, lead barrels would introduce a contaminant to any food or alcohol they contain, and lead cups would put the contaminant directly on a person drinking from them.
But conversely, there are a lot of materials that help to keep contamination under control. For example, copper, zinc, silver, and titanium have all been discovered to have anti-microbial properties that inhibit contamination that spreads across them. So for contaminants with the appropriate [MICROBE] tag (or something similar) they should be stopped by the use of the appropriate surface. A copper or brass pipe used in a screw pump would purify the water that comes through it (as opposed to all screw pumps doing this.) Copper or brass doors would stop creatures spreading contaminants across when them when they open them. Titanium surgical instruments would reduce infection probability among doctors who need to preform surgery or suture a wound.
Even if dwarf society is ignorant of modern medicine, any society that is exposed to these materials enough eventually learns that some are better for some applications than others (even if they ascribe it to something like certain materials being "lucky" for certain applications) just due to trial and tragic error.