Why is mysqlhotcopy slower compared to rsync?
rsync does not have any MySQL-specific gotchas to watch out for. rsync can copy literally anything with impunity.

mysqlhotcopy has to watch for opportunities to lock files which could delay actual start time for copying.

I wrote an earlier post contrasting rsync and XtraBackup along this line of reasoning

I also wrote a post on how to copy using rsync on a running mysql server with relative brief downtime.

Here is post I made in ServerFault

Here is still another post in ServerFault, with sample code !!!