What percentage of research papers have been digitalized?
Not an expert, but I would argue that this would be neigh impossible to determine given the criteria:


Definition of 'research paper'. As you stated, this needs to be defined, would this only include peer-reviewed? Published in a reputable publication medium? 
Definition of Digitization. Would microprint count? How about magnetic tape? Without a means of know what is and is not digitized, an accurate count would be impossible.
Knowing the upper limit of all knowledge, known-knowns (such as Google's Index of papers) Known-Unknowns (such as closed-circulation repositories), Unknown-Knowns (some repository that exists but the researcher doesn't know about), and unknown-unknowns (perhaps a hidden server in a soviet bunker from the 80's).