Models are not perfect and many factors in models will be changed.
Yup.
There's no methodology. It's completely assumable. In a way, it does make sense, but as said by tranthidung, I guess that people will be aware of their keys and protect them in the distant future.
I'm referring to the article that you've linked, which references the research paper for the value.
Based on our own methodology used in prior research, we were able to relate the difference in Calculated Market Capitalization and Price to lost coins. We can estimate that since 2010, about 4% of the Available Supply of bitcoin has been lost each year. This puts the current Available Supply at about 13.9 million coins, well below the 18.3 million Total Supply figure publicized. This means that about 28% of all bitcoins have been Irretrievably Lost.