Do academic journals check plagiarism against papers in student repositories?
Why would you care? The real issue is whether your paper contains plagiarism or not. Remember, by the way, that plagiarism is "presenting the words and/or ideas of other people as if they are your own". Turnitin and similar systems are advertised as "plagiarism checkers", but that's marketing. In reality they check for text overlaps, but overlaps do not necessarily constitute plagiarism. Overlaps can appear due to heavy use of cliche phrases or extensive but proper citing of others' works. Yes, universities sometimes take these "plagiarism scores" at face value and can reject your submission without looking further. It makes sense, unfortunately, as high plagiarism scores in case of student essays/term papers/etc. almost always appear due to blatant copying. 

Scientific journals and conferences, on the other hand, are supposed to do a more rigorous job. They can (and sometimes they do) check incoming papers with automated systems (since blatant copying happens in this world, too), but they really then must look inside and uncover the real reason of this high score. If you indeed present the ideas of others as your own, that's bad. Otherwise the editors might complain about excessive quotations or lack of original content, but that's another issue, not directly related to your question.