I'm fairly new to Studio One 3
I stumbled onto this the other night.
I assume that you are using the "cue" mixes as headphone sends.
Hidden behind the Main Output channel in the mixer view are the cue mix master sends.
You need to click and drag to the left of the main out to expose them.
Each cue channel has a volume control for the metronome
This is really pretty clever. You can send the click to only the headphone mix of the players that require it.
I hope that this helps.