Yes it should, so that is actually telling you that the noise you are hearing is not due to dirty power.
Some reasons you might be getting noise:
Some amps are noisy,
old tubes,
loose earth or bad connection in your guitar,
poor quality leads,
microphonic pickups & low battery in active pickups.
standing too close to your amp,
playing an amp loudly,
high gain settings.
The list goes on. I doubt that you will notice any different in sound whether you have the power conditioner on or not. The conditioner will filter out certain events like radio interference and spikes/surges, but they are only one small reason for noise in a system. You might want to try a noise gate if you aren't using one.