Hi @Julian Blechschmidt ,
To the best of my knowledge, I am afraid this is currently not feasible.
As regards to "Search-Mailbox", "-MessageClass" is not a valid parameter according to this article. Reviewing the linked article of the "-SearchQuery" parameter, we can learn that there's no searchable property for message class "IPM.Note.SMIME". The same conclusion applies to eDiscovery as well. eDiscovery does have a searchable property "ItemClass", but it's used to search for specific third-party data types and IPM.Note.SMIME is not a valid value of it, see this article.
Given this, I've just tried reposting this into the official feedback portal for Exchange Online. The link will be left below in case you or other community members would like to vote or comment there. Hopefully this can come true in the future.
https://feedbackportal.microsoft.com/feedback/idea/185930b5-e6fd-ed11-a81c-000d3ae5b6f4
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