A directory /var/www/owncloud/data/{user}/uploads/ has maybe 13GB, I need the space. May I delete these files?
Depends what this folder is in your setup.
That is not a default folder in the owncloud setup. The files a user uploads are typically in the data/user/ folder.
Check your config.php and other config files for that path, and if it's not set anywhere as something important, I can't see why you can't delete that folder.
This is the folder where chunks for chunked uploading are saved.
10.0.4 will come with an occ command which cleans up these folders.
./occ dav:cleanup-chunks
For the time being you can manually delete folder which are older then lets say one week
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