Can I copy files directly into a users data directory on the server?

I have an owncloud installation I want to migrate to NC11, however, since I have some trouble with that old configuration, I plan creating a new NC installation and just copy all the files (which are actually stored in only 3 user accounts, so copying on the Linux server system is not a big deal) . The question is: when I copy the files (using rsync to keep that timestamp of the files) in the users data diretory, will that work? or is it required that all files are copied in there using a NC-client or web-interface?

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It won’t work.
The files need to be worked with the Mysql service/Nextcloud instance.

You need to use Webdav Connection or a Nextcloud Client.

Ok, I expected that. How can I copy thru Webdav or a Client by keeping the timestamps of the files?

Normaly you can still use rsync, but use rsync to write into the Nextcloud folder of the client.

…which only works on a Unix-system on Client-side

Although you can try to do a manual rescan via occ in the CLI if you copy the files manually into the data folder. Then it should index the files into the db.

that would be the way I prefer, but since I do this whole thing only to get rid of all the mistakes I made in the past, I want a safe way. Are you sure this works without any trouble?

No. The only safe way which is supported by NC is webdav or the NC-Client itself. Everything other than this is at your own risk.