I THINK what is happening is that that form of open means your perl program and ssh share the same STDIN. And that ssh is the one flushing STDIN.

But i cant find a reference to this right now. I do know that if you didnt redirect STDOUT (and/or STDERR) your perl program and ssh share those two files as well

What might test that is  open(H, "echo '' | ssh $_ 'uptime' 2>&1 |");. In that case the shell is redirecting the STDIN of ssh

edit:another way to test this theory (redirecting the STDIN of ssh) would be  open(H, "ssh $_ 'uptime' </dev/null 2>&1 |");.