Concerning Akeeba, I am pleased to see that you successfully used it.
3) I can not tell you how Akeeba save the symbolic link present in the slave site.
I suspect that it will backup the files and folders corresponding to the slave site symbolic links. Normally, you should only backup the links and not the data.
Concerning specific Akeeba backup, I can just suggest you to ask Akeeba.
We never been able to use it with success.
This is the reason why you will find in the FAQ a procedure with a manual backup and also a shell script that allow performing a backup with native linux command.
www.jms2win.com/en/faq/faq-joomla-multi-sites#cat-268