This is covered in the ContentVersion documentation as by design:
Note: Depending on how files are shared, queries on ContentDocument
and ContentVersion without specifying an ID won't return all files a
user has access to. For example, if a user only has access to a file
because they have access to a record that the file is shared with, the
file won't be returned in a query such as "SELECT Id FROM
Your previous edit on your question mentioned the
I, through a record the file is shared with, which is specifically mentioned in the quoted documentation above.
You can also see the following answer that goes over this accessibility of content versions in queries as well.