JTAS articles are not canonical for the OTU unless the article in question is written by a GDW staffer explicitly for the OTU or the article itself is 'approved for use', most of them match this criteria.
Marc's robots series of articles for example are canon, the article about special psionic talent use isn't.
I'm not sure it is that simple. Partly because of the differences in articles that add to the toolkit of CT (and later MT and TNE in Challenge) and those that are expressly about the setting, and the fact that some articles blur the line considerably. JTAS was also a big player in building the early OTU's elements, and not all of those early elements made the grade.
Canon is also inherently fluid in several ways. The most common recognized fluidity, as Aramis reminds us periodically, is between editions. There is also the shifting opinions and developments of Marc to lend fluidity (the Annic Nova being a prime example). The other, less recognized fluidity is that the setting is simply too big to be uniform, no matter what some folks want to believe. Statements about ship classes, port organization, precise noble organization and forms of address, and myriad other little details that we choose to glean from single published examples are not necessarily true across the entire Imperium, or even an entire Domain or Sector.
A general statement about GDW's JTAS is hard to produce, except that, having all passed through the judgement of GDW directly, setting elements in JTAS are more likely to be Canon than elements that appeared in other periodicals. The Keith brothers were an important part of that early setting building process, and their material retains a higher degree of Canonicity because of that. Is every last word of theirs Canon? Do you even have every last word to look at? They contributed in some very subtle ways and in some less well known places.
The best, but not easiest, answer is that the question needs to be asked about each item.
