Looking at 2015 (other years are comparable), ~60% of the people are identified as being in an MSA, either central city or balance of MSA. Of those, the MSA is missing for 51%. Why is MSA missing so frequently?
In the ATUS sample the METRO and METAREA variables are identified by the US Census Bureau and are released with the public use files. Many MSAs are not identified because the US Census Bureau did not identify them in the original public use files. One reason for this may be a population size restriction made for confidentiality purposes. If you cross-tab METAREA with MSASIZE while restricting METRO==1 | 2 you should notice that there are no MSAs identified with a population of less than 250,000.