Clockwork 'Disable Night Vision' setting is incompatible with Shortcuts mod 'Enable Night Vision' setting. If it is Off.

The same setting is incompatible with Bob's Night Vision modules (There are 3 tiers)

For compatibility, wouldn't it be easier to disable the Night Vision items via the NightVisionEquipment prototype, rather than try to remove all the items and technologies?

Looking into the Prototype,

desaturation_params - Set the visual display to not do anything, combine with "energy_source" and "energy_input" to prevent the module drawing power

Well, it's just that having NV disabled makes the research a pointless resource sink (and building the module as well). Preventing the module from drawing power is how it currently works (should you have existing modules before adding Clockwork or enabling the option), since Factorio will crash if the nightvision module is removed entirely. Anyways, thanks for the heads up - I'll look into adding compatibility support when I have a moment.