Question
Why there are two locations for domain logs: /var/www/vhosts/system/example.com/logs and /var/www/vhosts/example.com/logs?
Answer
The directory /var/www/vhosts/system/example.com/ contains domain configuration, its log files, statistics data and protected directories.
By design, this directory is not accessible in Plesk interface.
Therefore, to allow accessing the domain logs from Plesk interface, the hard links (the files that have the same inode) to the files in the directory /var/www/vhosts/system/example.com/logs are created in the directory /var/www/vhosts/example.com/logs.