The effect of the slowdown on the total handshake time wouldn't work well for detection, since without a baseline you can't tell if it's slow due to the backdoor, or due to high network latency or a slow/busy CPU. The relative timing of different steps in the TCP and SSH handshakes on the other hand should work, since the backdoor should only affect one/some steps (RSA verification), while others remain unaffected (e.g. the TCP handshake).