How are citations used to fairly compare researchers: fewer publications and fewer co-authors versus more publications with many co-authors
A general rule of bibliometrics is that they shouldn't be used to compare people (or projects, or papers, or research projects) across different fields, because publication culture can vary wildly even within disciplines and between closely allied fields. To begin with, the size of the field - the number of papers published per year, for example - has a direct impact on how many citations each paper gets.

Your quandary is an example of this. In certain fields such as high-energy physics, astronomy, or parts of biology, a lot of the science is concentrated in very large collaborations, which produce papers with many citations and many authors. It is indeed unfair to use citation counts to compare such a CV with, say, a mathematician's, since papers there tend to have few authors and, in many specialized fields, be read by very few people indeed, even for high-quality papers.

Whether such bibliometrics are used in practice by hiring committees - well, that obviously depends on the field, the institution, and the specific people involved. If all the applicants are from similar fields then this may not be a huge problem, but the numbers need to be treated with some distance to avoid the problem you point out. If a hiring or review process places a large emphasis on citation counts (or other bibliometrics) for applicants from different fields, then that is indeed a problem.

One final thing you should keep in mind is that applicants with a high-citation-count, large-collaboration paper in their CV are likely to get asked at interview questions like


  So, what was your role in this collaboration?


in any case, as part of the interview process.