Medical Testing for Malnutrition

There are doctors who sometimes answer questions here who can give you a more detailed answer. Blood tests can tell nutritional deficiencies, they can show low protein levels, potassium, calcium, which vitamin levels are low. There are also bone density scans, though the person's age is a factor in that.
Are you looking for specific clinical consequences and trying to factor what tests would show that? If you are, I'm sure people here can come up with the tests you'd need.

I know a lot about B12 deficiency, because I have a disease that makes me unable to absorb it through the digestive system. B6 deficiency comes along with that.

There are tests for those, yes It gets a little complicated. A blood level of B12 is not always sufficient to confirm diagnosis of the disease. So they do other tests, too, but they won't do those without symptoms, typically.

It's a serious disease to have, actually. Not after treatment usually, but if they don't Dx it.

They can't do much in office, the first steps of diagnosis would be made by observation, if the patient had symptoms of nutritional deficiency they would do a blood panel. If the blood work showed further signs of malnutrition they would order more tests, possibly requiring a visit to the hospital depending on the problem.

It's a rather complicated topic and matters a lot on the age of the patient. In the very young, you can tell on physical exam. As the protein gets depleted you start to see muscles and bones that you shouldn't be able to see. Eventually the protein is depleted to the point that there aren't even the normal intravascular proteins that by osmosis keep water inside the bloodstream. At that point people's belly's will swell, not because their stomachs are full, but because water is swelling the belly outside of the intestines or blood. The simplest and cheapest test with what I found to be the best prognostic inticator was a protime. If you are not on anticoagulants and your protime is elevated, then you are probably so malnourished that your body is sacrificing clotting factors to keep you alive. Others preferred a total protein, but that varies so much from individual to individual that I felt it was only predictive if you had a series of them to compare. Protime (you probably won't find it in literature) was in my experience the cheapest and easiest test to do with greatest predictive value across all races and ages. It's an end stage indicator, but probably that's why it was so reliable.

It's a blood test sent in a blue top tube (unless they changed the color coding on the tubes in the last 5 years). If you use this, I suggest you have a young attending derisively ask the old codger, "What century were you born in?"

To which the geezer smiles confidently and says, "Not century, but millenium."

Which test to order mainly depends on which nutrients are expected to be deficient, and this depends on the suspected cause of malnutrition: strict vegetarian diet, chronic alcoholism, anorexia nervosa, starvation, chronic bowel disease, intestinal parasites...

I have worked in hospital labs as a "clinical laboratory scientist" and two important tests are total protein and pre-albumin. Pre-albumin is a more "specific" test for malnutrition. I've seen it ordered often on children and folks in nursing homes, and patients that have been in the hospital for a long duration.