I’m going to agree that tracking whether the characters are meeting their RDA of different nutrients seems a bit excessive.
I realize my previous suggestion is more complex than what we currently have, but it’s still simple enough to be easy for anybody to pick up and understand; the basic premise is lifted from another roguelike which handles it in a very similar fashion and it’s quite intuitive.
Taking it further and back to the original concept, malnutrition does seem like a neat idea to implement, and I can easily see how to do so really easily while fixing the cold/flu problem at the same time: the current system assigns different foods a ‘healthiness’ value which seems to already correlate with the nutritional quality of the food. Currently when your invisible ‘healthiness’ stat drops low enough (and it’s always slowly dropping) you run the risk of catching a cold or the flu - that’s the game function of vitamins, they dramatically increase that hidden stat and stave off the risk of randomly catching those syndromes by raising that hidden stat in the same fashion as eating a ‘healthy’ diet. Note that some foods like junk food type things can even lower that hidden stat when you eat them.
What if instead of randomly catching the cold/flu syndrome when that hidden stat drops low, instead when it drops to a low enough threshold it’s guaranteed to give you a ‘malnourished’ syndrome that hurts your attributes or something and doesn’t go away until your ‘healthiness’ stat improves? To me, at least, this makes sense: eat junk food and nothing fresh, green, or nutritious and eventually you get weaker and slower until you get better quality food or at least start supplementing your potato chip and soda binges with some vitamins. It also gets rid of the weird thing where you catch a cold or the flu when you haven’t been in contact with any vectors for them. Perhaps in such a case we could save those syndromes in the code for once NPCs are in place and it would be more appropriate to come across human contact-specific diseases.