Hey, sorry for not getting back to you for a while, was busy doing finishing touches for the new update: [Beta] Midihub Editor 1.12.0 & Firmware 1.12.0, which I’m sure would have been useful for you to have a few days earlier (because of the new MIDI monitor) 
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Yes, you may map the Bypass argument to a MIDI CC to enable / disable the pipes. You may map multiple Bypass params of a few pipes to a single CC knob.