if you have the Scriptrunner-Plugin for JIRA you can add a scripted custom field, e.g. "Number of Labels". Use the Number Searcher for the field.
This field is defined with the following script:
Then, do a full reindex, so the field is filled for all your issues.
After that, you can search with the following JQL:
"Number of Labels" > 2
But, this works only if you have the scriptrunner plugin. I don't know a solution without that plugin.
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