Properties are not saved with monticello, though. They are like method properties. So one would
need to build something on top...

I don't know about MC model, but maybe extending MC to support properies/annotations could be a path?

Yes, that would be a possibility. Adding things to the monticello .zip is easy (and easy to ignore later/by others).

Another idea would be to make a subclass of InstanceVariableSlot that stores the note in a property but
it is actually part of the slot definition:

Object subclass: #Point
slots: { #x => InstanceVariableWithNote note: ��this is useless��.
#y }
classVariables: { }
category: 'Kernel-BasicObjects'

As the note is part of the slot definition, it would be saved in Monticello.

It could be silly question but most of the time I wish to annotate while debugging, using that option would affect my debugged objec state?

No, the current class builder would migrate the objects (I think). As this does not change the shape of the instances, even that can be avoided.