Thank you for your interest in our service. Let me address your questions:
1. SyncMate is capable of syncing any amount and size of files and folders, as well as sub-folders underneath. However, synchronization of such big number of files can take quite a while. But, I am also happy to inform you that only the first sync attempt will be rather long, all subsequent synchronizations will be much faster, due to the fact that SyncMate checks the information relevance according to own logged sync history.
2. By default, SyncMate exclusion filters are configured to ignore all hidden files and folders (which name starts from "." symbol). However, you can easily disable this filter in "Folders" plugin configuration.
3. You can configure SyncMate to allow connections only from certain list of IP addresses or manually allow each connection to be established. You can also password-protect the incoming connections for additional security.
The detailed user-guide for SyncMate 4, describing all software options and configuration can be found at our wiki:http://wiki.eltima.com/user-guides/syncmate-macos.html
Hope this information helps.