I can't remember what it's actually called, but there is something like "blood oxigenation", which I believe is something that changes relatively quickly depending on a number of factors, and can be measured in some non-invasive way. Maybe looking into this and using it as a "stamina" level if applicable would work?

Food variety is an important thing for long term missions such as a Mars expedition, so I'd say that the large number of different food types avalable adds to "realism" as such. Revising their calorie count would probably still be beneficial for those really low ones. However, that would effectively mean more food being available (same amount of items spawned with more total calories combined) so that would, on the other hand, lower difficulty. One way to somewhat compensate this could be to review the weights of the various food packages and slightly increase them, especially the ones that give more calories? I never really looked at the current weights and how "realistic" they are, but maybe it would be possible to "sneak in" a bit of extra weight here and there.

In terms of calories while on EVA, I was thinking more along the lines of "energy drinks" (not the "caffeine overdose" kind), which give less hydration but also some calories. Maybe even a way to combine items like that "orange drink <something>" with water to make these kinds of drinks from the low weight packed dry component and the water produced on site?

I also think that being able to save text notes in the Datapad, which can either be attached to discovered permanent locations or photos, or can be "unattached" generic notes/reminders for yourself, would be useful and also be in line with the "keep track of some things on your own" approach. In games like this, where you have a large area to cover with various things to remember, you either have a good memory, or make out of game notes. But the player character here has a portable computer which lends itself to record such information within the context and world of the game itself.

A relatively simple, barebones warning system could be simply to change the screen content of the terminals used to access the hab status screen. Eg. current white text on black bacground - everything's ok, red text on black background - something's offline, use me for details! Maybe an in-between (yellow?) state to indicate that a part slot sowehere is below a certain threshold and should be looked into (but this would need a much more complex polling of all hab systems and slot states).