The main pro is that people find it incredibly useful to be able to label and then search and report on free-format labels that suit themselves.
The downside is people can't type, or try to be clever and you end up with a lot of singleton, or meaningless labels. You will always find some people overdo them (labelling an entire project for example) as well.
If the second point becomes a problem, you'll usually find inexperienced Jira admins screaming for control over labels, limiting them for users and hence making them pretty much useless - if that is the desire, then just create a multi-select list for labels.
Where I think Jira lets labels down is not controlling them, but providing decent tools for admins (or ideally, project admins) to monitor and quickly fix them. There are, of course, tools on the marketplace for that as well
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