rsync will use the same data stream for all the files. After the initial sync up, only file changes will be sent. I wouldn't worry about bandwidth throttling unless you routinely make huge changes to the the directory tree you are backing up.
Rsync uses a combination of timestamps and checksums to identify which files have changed and where the files have changed. For log type files there is some syncronization overhead and then the tail of the file is transfered. There should be some slowdowns in bandwidth utilization when files have changed as files need to be read and checksummed at both ends. These may be sufficient to keep bandwidth throttling from kicking in.
rsync backups can be interupted, and resumed later. It will then proceed to backup the current changes including any missed changes from prior runs. If you have a large file to backup, frequent interruptions may not work. You need to let it run long enough to transfer the file. Any strategy based on frequent interupts of the backup are likey to fail.
ssh is encrypted and should be exempted from throttling, although they may throttle it for large packets. If they are throttling on packet size, you will get throttled no matter how frequently you interrupt the process. As you are likely transferring only small part of your directory structure, throttling should still leave you with reasonably fast backup.