We use Nagios to monitor quite a few (~130) servers. We monitor CPU, Disk, RAM and a few other things on each server. I've always used SSH to run the remote commands, purely because it requires little to no additional config on the remote server, just install nagios-plugins, create the nagios user and add the SSH key, all of which I've automated into a shell script. I've never actually considered the performance implications of using SSH over NRPE.

I'm not too bothered about the load hit on the Nagios server (It's probably over-speced for what it does, it's never been over 10% CPU), but we run each remote check every 30 seconds and each server has 5 different checks performed. I assume SSH requires more resources for each check but is there a huge difference? (I.E. enough of a difference to warrant the switch to NRPE).

If it's any help, we monitor a mix of physical servers (Normally with 8, 12 or 16 physical cores) and Amazon EC2 medium/large instances.