There is no good way to do this currently, I would not advise you to try storing extension specific info on nodes - the graph should contain only information related to execution.
What we should do is give extension authors a way to serialize information into their own extensions object in the file. Unfortunately that does not exist today.
For now I would serialize this information in another file which users will need to keep around with their graph - I would think about this like any non code config file in a solution or project.