Should you thank helpful referees in the acknowledgements section of a paper?
I usually try to add a line to the acknowledgements to thank anonymous referees and I try to make it honest and clear. Reviewers' time and effort invariably improves my papers and I think it's only polite to thank anybody who contributed for their time, effort, and engagement to making a manuscript better.

Will anybody care if it's missing? Will anybody even notice if it's missing? Probably not. That said, although it may be the "job" of the reviewers to give suggestions, refereeing is something that academics do as volunteers. Reviewing papers is perhaps the most thankless part of an academic job. Acknowledgement of the positive impact that referees have seems like the least an author can do.