So Proxy torp and critical shot can both fire at a vessel after it has cloaked if the vessel that is cloaking is targeted before it cloaks. Or when the vessels move into range to fire after it has cloaked.
Example:
I order proxy torp to fire on a vorcha while they are out of range -------- vorcha cloaks out-------- Monsoons get into range and still fire at the cloaked vorcha.
To me that sounds like it might be an update on the proxy torpedo, like the crew targets that location in space and not the vessel, after all it is a Proximity torpedo.