fix(manifests): remove emptry CRD and reference

[zdtsw]

Issue link

backport fix from opendatahub-io#49

What changes have been made

Verification steps

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• I've made sure the tests are passing.
• Testing Strategy
  • Unit tests
  • Manual tests
  • Testing is not required for this change

[dimakis]

/approve

[dimakis]

/lgtm

[openshift-ci]

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