There are a couple issues that need to be addressed when attempting to answer this question, namely,
First, it is important to note that Emacs is a text editor is used by software developers so this answer should be considered in the context of users who may use Emacs as their primary tool for their job, i.e. several hours a day for several days a week.
With regards to the question of if Emacs causes "Emacs pinky", I could find no scholarly articles on Google Scholar when looking specifically for "emacs pinky" and the search results when "pinky" was dropped as a search term were also of limited usefulness. Similar searches using Academic Search Premier at a well known research university also resulted in no results being returned. As such, it is reasonable to conclude that as of August 2013 no studies have been published that link Emacs and RSI.
However, a number of neologisms exist for RSI such as "BlackBerry thumb", "gamer's thumb", and so forth. So if we consider "Emacs pinky" to be a neologism for any RSI that is encountered by Emacs users then the question changes to if heavy use of Emacs may lead to an RSI. As shown in the body of the question, it appears fairly well established that Emacs users refer to RSIs as "Emacs pinky" and this also supported by such sites as the EmacsWiki.
Links between typing and repetitive strain injuries is fairly well established and has been reported,
In a preliminary report issued earlier this year, NIOSH-Michigan
researchers found that 40% of more than 800 employees surveyed
reported symptoms of RSI, including pain experienced in hands, wrists,
elbows, shoulders or neck.
The study was jointly requested and paid for by Newsday and the
Graphics Communication International Union Local 406, which represents
about half of Newsday's and New York Newsday's 3,100 full-time
employees. The study, the first comprehensive survey of RSI in the
newspaper industry, concluded that computer-terminal use at a
newspaper office presented "a hazard" to workers' health.
Although it might not be linked to specific types of RSIs like Carpal Tunnel Syndrome.
Finally, we must also address the situation in which "Emacs pinky" is not a neologism, but a very specific type of injury. In that case we must again defer to the lack of studies that have been conducted to determine if Emacs is linked specifically to RSI in a users pinky. However, it is difficult to conclude if "Emacs pinky" is supposed to refer to a specific injury to the pinky since most anecdotes refer to general RSIs of the hands.
A number of reports on the internet (one, two) that indicate that users of Emacs experience pain in their left pinky that they attribute to their use of Emacs due to the use of the Ctrl key for a number of commands. Assuming that these users are being honest in their reporting then these reports do provide us with a body of evidence that something is happening. In this case the hypothesis that the heavy use of the Ctrl by heavy users of Emacs causing pain in the left pinky is not unreasonable.
So to summarize, no studies have been conducted into Emacs use to determine if it causes a specific RSI that affects the pinky. It has been established that typing can cause RSI in which case the claim is valid if "Emacs pinky" is a neologism for RSI in general.