Is there any scientific reference about position of the LGBTQ community in STEM academia?
The basic answer is that there is very little hard data. One study that I did find (via ResearchGate - I didn't have direct access if it even exists) is "Factors impacting the academic climate for LGBQ STEM faculty", Eric V. Patridge et al., Journal of Women and Minorities in Science and Engineering 20(1) 75-98 (2014).

Several quotes stand out: 


  Amid the current nationally led campaign to increase the STEM workforce, there are numerous
  institutional efforts to support women and underrepresented ethnic minority STEM professionals;
  however, virtually none of these focuses on LGBT communities.


and


  A survey of the literature reveals that
  data-driven research of LGBT communities has been restricted to the social sciences, humanities,
  and health fields; there are only a handful of publications focused on LGBT communities in the
  STEM fields, and none of these are based on empirical data. Qualitative academic discussions
  report that LGBT populations are discouraged from entering the STEM fields because heteronormative
  climates are so widespread (Bilimoria and Stewart, 2009; Cech and Waidzunas, 2011;
  Gunckel, 2009). Our analyses support previous discussions...


The data in this 2014 paper was drawn from a 2010 study. Of some 5000 respondents, 498 were faculty. Of those, 59 were from STEM. After some further down selection, they ended up with 47 STEM faculty.

Points of some interest include: 


  In response to questions on internal experiences and identity, STEM faculty (n = 47) reported
  the highest level of discomfort across the three questions included in the survey (campus, department,
  and classroom) (Table 3), although these differences were not significant. Notably, faculty
  from STEM departments reported significantly higher levels of professional outness than did
  those from other departments [2(4) = 16.7, p &lt; .01].


However, 


  the more out a STEM faculty member, the more likely it was that he or she
  was uncomfortable.


and, relative to all faculty in the study,


  STEM faculty members (n = 47) were most likely to consider
  leaving their institutions (53.2%)


Further,


  Our analyses support the hypothesis that heteronormative climates contribute to LGBQ faculty
  members seeking alternative employment options, and department level analyses suggest this
  closely describes LGBQ STEM faculty.


In addition,


  The loss of current and future faculty mentors for LGBQ communities is particularly problematic
  because there are so few resources that support LGBQ students. While there are countless
  organizations dedicated to the development of women and minority STEM talent, there are
  only two national organizations that encourage the development of LGBQ STEM talent.


In Physical Review Physics Education Research there is a paper titled "Enriching gender in physics education research: A binary past and a complex future", which touches on needing to look more broadly than just men/women. However, it does not appear to have any useful data on LGBT in physics.

Much of the rest I can find is online, non-peer reviewed studies. While interesting reading, it is harder to draw conclusions much less figure out what to do. 

(As a response to your addendum to the question - it is quite clear that the person described in the New York Times Op-Ed piece was indeed, and sadly, afraid to reveal their piano playing. I can easily imagine that behavior coming from long experience with negative responses over time which have little to do with playing the piano. You might be interested in Gay and in STEM Fields which rebuts some of the points made in the Manil Suri op-ed piece you reference.)