Edit: While it was running (at any point between 1932-1972 when the whistleblower came forward) to what degree was it common knowledge amongst medical professionals?
Edit 2: Schatz, not Shatz.
There's some confusion in the question premise: there were quite a few papers, with titles generally including the phrase "Untreated syphilis in the male Negro", so it isn't hard to pull up most of the lot. The papers were not "hidden" and were published in venues including
American Journal of Syphilis
Journal of Venereal Disease Information
Public Health Reports (a long running journal around since 1878)
Journal of Chronic Diseases (on Elsevier)
Archives of Internal Medicine (now known as JAMA Internal Medicine)
Importantly, the articles did not make the nature of the experiment clear and in fact tried to be actively deceptive. There was a strong impression carried that all participants were volunteers, and even said outright it was composed of "people [who] responded willingly". It takes some careful reading to realize something might be off. As an example, let's consider Environmental factors in the Tuskegee study of untreated syphilis: Untreated syphilis in the male Negro (1954) from the wide-reaching Public Health Reports.
This particular paper sidesteps even mentioning if the participants were informed, with paragraphs like
For the men in this study medical care has not improved appreciably in the past 20 years. The men still rely on home remedies and old superstitions to cure their ills. Excellent medical facilities exist within the county, but either the cost makes such care prohibitive to this low income group or the patients are unaware of their availability.
On a brief read, it might appear that those who have not gotten treatment have done so in a willing sense, being reliant on "home remedies" and not even being aware of treatment. On contemplation ... why would you not tell them about treatment? To be clear, penicillin was not a treatment when the study started in 1932, but by 1954 -- when the paper was written -- penicillin was well-established as working on syphilis. The paper fails to mention the amount of outright lying that was required to start and maintain the state of affairs (lying about the nature of the initial tests, giving fake treatment, contacting the military during the WWII draft to keep most of the people in the study out since military service would require testing and treatment for syphilis).
The first person to pick up on the issue and object to the study was the Georgia physician Count D. Gibson in 1955, listening to a talk of Sidney Olansky (one of the three main caretakers of the study starting in the 1950s). The talk (as opposed to the papers) made clear treatment was being withheld. Gibson read all the published papers and wrote Olansky, pointing out the omission:
The ethical problem in this study was never mentioned. . . . There was no implication that the syphilitic subjects of this study were aware that treatment was being deliberately withheld.
He then pointed out the study violated any of the common codes of ethics: Hippocratic, Maimonides, the Golden Rule, and the AMA Code of Ethics.
Olansky responded in a letter:
I’m sure it is because all of the details of the study are not available to you.
and tried to justify the study in that those in it "knew that they had syphilis & what the study was about" and that a nurse "takes care of all their needs" and that "any patient in need of medical care [for syphilis] or any other reason was treated" (leaving out the fact that this was referring to the very early stages of the study only, this was done before penicillin was known as an effective treatment, and the treatments that were done were stopped in order to avoid "contaminating the data"). Some later patients did get penicillin (as Olansky explicitly claims) but the letter leaves out this was only done in scattered cases and there were concerns (again) about contaminating the data.
Gibson was still "disturbed" by the response and was told at the Medical College in Virginia
... that if he wanted to get along, succeed and thrive in his medical career he’d better shut up about this and stop raising questions. He was going up against very senior and powerful men.
Schatz (who the question is about), found out about the study from a 1964 Archives of Internal Medicine study, "The Tuskegee Study of Untreated Syphilis The 30th Year of Observation", which buries itself in clinical details:
As of Dec 1, 1963, approximately 59% of the syphilitic group and 45% of the control group were known to be dead, and the average age of the survivors in each group was 65 and 66, respectively.
Approximately 96% of those examined had received some therapy other than an incidental antibiotic injection, and perhaps as many as 33% have had curative therapy.
Schatz realized what was going on and was quite direct:
I am utterly astounded by the fact that physicians allow patients with potentially fatal disease to remain untreated when effective therapy is available. I assume you feel that the information which is extracted from observation of this untreated group is worth their sacrifice. If this testimony is the case, then I suggest the United States Public Health Service and those physicians associated with it in this study need to re-evaluate their moral judgments in this regard.
The letter was buried and never responded to.
Where momentum got going was Peter Buxtun (in San Francisco) who picked up on a story from a workmate, who had taken in a patient with insanity and syphilitic infection, which was immediately treated with penicillin. The patient turned out to be from the Tuskegee group and the doctor was contacted later by the county medical society:
‘See here doctor so and so,’ I never knew his name, ‘you have spoiled one of our subjects. You have treated someone who was not to be treated.’
Buxtin talked over this with colleagues, but they were unconcerned; one of them pointed out how it stated in the study that they were explicitly "volunteers with social incentives". (Hopefully I'm getting across how people were getting snowed over. Incentives included hot meals and treatment for other diseases. The "informed" part of the consent is missing.)
Buxtun was quite persistent in digging into what was going on, with multiple meetings; I won't detail every point, but one of the claims to justify keeping the study going was that treatment this late in a latent syphilis would somehow now be harmful (this isn't true). Eventually, it took his speaking to the reporter Edith Lederer with the Associated Press (multiple times, it was a complicated story) with the story eventually going out on July 26, 1972 as
Syphilis Victims in U.S. Study Went Untreated for 40 Years
and then, suddenly, everyone knew. The study finally was ended November 16, 1972.
...
Reverby, S. M. (2009). Examining Tuskegee: The Infamous Syphilis Study and Its Legacy. United States: University of North Carolina Press
Reverby, S. M. (Ed.). (2012). Tuskegee's truths: rethinking the Tuskegee syphilis study. UNC Press Books.