It does so for scripts absent in the Main section but present in other sections when searched by the base named commandID inferred from named commandIDs of the script instances present in other sections, e.g. by
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isolated from
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of an instance in the MIDI Editor section.
This renders impossible finding out if a script instance is present in the Main section.
For other sections it returns commandID searched by inference even if a script instance has been removed but REAPER has not yet been restarted for the new data to be loaded from reaper-kb.ini which updates in real time.
I understand that's not a bug and the base named commandID is presumably a placeholder/template for instances in other sections, and there're alternative methods, but would be useful if it worked consistently (from the user perspective)