The server files can be copied in this way, yes. Though this is less important since they are easy enough to recover (re-download the source and compile a fresh core).
For the DBC and MAPS etc, they are just files. You can back these up using the same method as for the server files, but again, you can just extract this information again so not a big deal if you lose it.
The one thing you will need to backup is the databases. Specifically the auth and character databases since they contain all the account, character and guild info. The world database can also be backed up, but this is less important since it will only give you which mobs are currently dead and when they should respawn.
To backup the databases, you can use mysqldump. See https://dev.mysql.com/doc/refman/5.7...mysqldump.html for details on using mysqldump for this.
For other ways to backup your databases see https://dev.mysql.com/doc/refman/5.7...p-methods.html