Hi @Iakovos Soulis ,
Thanks for the post.
According to the research, currently there is not possible to manage multiple documents with different permissions in your scenario.
Usually, when we manage a large number of items in single library, we create folders or document sets to make it easier to manage their permissions.
Currently there is no OOTB in SharePoint online to meet your requirement, you could send feedback to Microsoft SharePoint Feedback.
I hope I can offer you a better experience next time if I have a chance to work with you again.
Yours faithfully,
Renjie Sun
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