Whether to include a middle initial in author name on academic publications?
It's a matter of author's own preferences whether to include the middle initial or not. It's better to be consistent from the beginning, and do not use different styles in different papers, although the author might be able to "glue" together their records in some bibliographical services if they treat different spellings of their name as different persons (I have managed to do this on Scopus for myself, but there may be other databases which I don't know).

This, however, does not solve the main problem - it only reduces the chance that two authors will have the same name or initials, but it does not eliminate it completely. This is why authors are advised to establish ORCID:

Quoting http://orcid.org/, this is "a persistent digital identifier that distinguishes you from every other researcher and, through integration in key research workflows such as manuscript and grant submission, supports automated linkages between you and your professional activities ensuring that your work is recognized".

Some publishers already allow the author to specify their ORCID during submission, and some others already require it, for example PLOS One and the Royal Society.

Another useful feature of ORCID is that it allows the author to keep a public profile with a list of their publications (and other optional details). Even more, one could link their ORCID profile to Impactstory (https://impactstory.org/) and track online impact of their research. As an example, by now I've already stopped maintaining a list of publications on my personal homepage since I can just put there links to several databases, ORCID being one of them, and most of them (as reported by Impactstory) are in open access anyway.