After assigning VST3 effects plugins to custom keyboard shortcuts, changing the "Sort Effect Menu By:" setting (Edit=>Preferences=>Effects) will reassign the hotkey to other effects. Interestingly though, the hotkey menu will still show the old effect name (not sure if that survives an app restart or not).

Presumably Audition assigns an ID/address to the effect which is used while assigning hotkeys, but rearranging the menu rearranges the ID assignments. Obviously these two functions should be independent of one another.

Audition version: 12.0.1.34
Windows 10.0.17134