Is "doing everything in your head" a good proxy for intelligence? Suppose Bob never takes notes in class and just mentally "gets" a subject. Is this ability of mentally learning a subject without actively recording the information a good proxy for intelligence?
Subject performance is not intelligence: Doing well in a single subject is a weak measure of intelligence. While the correlation between IQ and GPA is fairly high. The correlation for a given subject will typically be much lower. So another way of framing this subject is whether doing a subject in your head is a good proxy for subject understanding.

More broadly, your question implies a few other questions:


Does note taking improve learning?
Are students who are either more generally intelligent or more capable in the subject less likely to take notes?
Is there an interaction such that the benefits of note taking is less for more skilled students?


1. Is note taking effective?
I assume that note taking is generally effective and helping students to retain the information presented in a lecture. It encourages students to focus on the material. Deeper information processing increases depth of learning and retention. It also provides a means of revision, which in turn should increase retention.

That said, there are a lot of different types of note taking. In particular, part of the skill of note taking is working out what is important and what is not important.

There are also many different pedagogical contexts. For example, in some settings note taking is required for keeping a record whereas in other settings slides or recordings of the lecture may be provided. Logic says that if note taking is the only record, then it would be more important. Similarly, lectures vary in the degree to which the specific material needs to be mastered as opposed to providing an overview and relying on textbooks or other activities to hone skills. I would assume that where a subject requires students to repeat or apply information presented in the lecture, then taking notes will be more effective.

2. Are students who are either more generally intelligent or more capable in the subject less likely to take notes? I don't know of specific research into this, but I think there would be two key factors operating. First, less capable students are more likely to use poor study skills. So this might involve either no note-taking or poor note taking (e.g., taking down too much information). Second, more capable students are likely to know more material and also be able to absorb the material better. So in some cases, they may have less need to take notes, which in turn may lead them not to take notes.  

It might also be related to self-efficacy beliefs which are only partially grounded in reality. So for example, the student might think that they are understanding more of the subject than they are, and fail to see the benefit that they would derive from taking notes.

3. Is there an interaction such that the benefits of note taking is less for more skilled students? Certainly at a certain extreme level of prior understanding where the student already knows all the material, then there may be little benefit from note taking. Likewise, as mentioned previously many features of the context may influence the need for note taking.  However, in contexts where the material is somewhat new to all students, and the test is on the material presented in the lecture, and there are no slides or other material I imagine that note taking would be fairly valuable for all students.

Some research:

It seems there is quite a lot of research on note-taking. Check out "note taking" on google scholar.

Hartley and Davies (1978) review note taking looking at why students take notes and the research on note taking.

Kiewra (1989) provides another review of the learning benefits of note-taking:


  This review article investigates the encoding and storage functions of
  note-  taking. The encoding function suggests that the process of
  taking notes, which  are not reviewed, is facilitative. Research
  specifying optimal note-taking behaviors is discussed as are
  several means for facilitating note-taking, such  as viewing a lecture
  multiple times, note-taking on a provided framework,  or generative
  note-taking activities. The storage function suggests that the  review
  of notes also is facilitative. Research addressing particular review
  behaviors, such as organization and elaboration, is discussed as
  are the advan-  tages of reviewing provided notes, borrowed notes, or
  notes organized in  a matrix form. In addition, cognitive factors
  related to note-taking and review  are discussed. The article
  concludes with an alternative means for defining  and investigating
  the functions of note-taking, and with implications for edu-  cation
  and for research.


References


Hartley, J., &amp; Davies, I. K. (1978). Note‐taking: A critical review. Programmed Learning and Educational Technology, 15(3), 207-224.
Kiewra, K. A. (1989). A review of note-taking: The encoding-storage paradigm and beyond. Educational Psychology Review, 1(2), 147-172.