that hook uses types by default to classify files

since your .meta files are not going to be classified as either yaml or json you need to either (1) rename them so they are (by adding .json to the filenames) or (2) override the filtering to manually work via filename instead

I would recommend adding a special hook and keeping the original one in place. using your example it would look something like this:

repos:
- repo: https://github.com/python-jsonschema/check-jsonschema
  rev: '0.27.3'
  hooks:
    - id: check-jsonschema
      # not necessary, but can be useful for `pre-commit run` if you have other `check-jsonschema` hooks
      alias: check-jsonschema-meta  
      name: Validate meta files
      args: ["--schemafile", "schemas/my_schema.json"]
      types_or: []  # reset to default
      files: ^data/.*\.meta$

disclaimer: I wrote pre-commit