Placing hyperlinks in text is a funny business. It seems like there are some reasonably well-accepted standards for what text you underline when you want to place a link (at least such that I had the feeling of a violation in the sentence above), but I can't find any explicit guidelines. Perhaps it's because the google keyword "hyperlink" is not very informative at all...
But here's my alternative hypothesis: I think we place hyperlinks with the same timing as we use pointing in spoken speech, and for the same function: to determine reference. So that would mean that the best place for a link to start is where you would start pointing in a face-to-face conversation. And there are very clear norms for how the timing of pointing works; folks like Herb Clark have studied this extensively.
Going back to my example above, imagine I was sitting in my office with a pile of issues of Journal Y on my desk and pointing to illustrate my sentence. Imagine the following examples:
(1a) A [point] new paper by X in Y shows Z.
(1b) A new paper by [point] X in Y shows Z.
(1c) A new paper by X in [point] Y shows Z.
(1d) A new paper by X in journal Y shows [point] Z.
My intuition is that 1a is most natural, with 1d far behind. 1b and 1c definitely are about reference to the author and to the journal. Similarly:
(2a) A new paper by X in Y shows Z.
(2b) A new paper by X in Y shows Z.
(2c) A new paper by X in Y shows Z.
(2d) A new paper by X in journal Y shows Z.
The same thing seems to apply. If the link to Y doesn't go to the location (but to the actual thing itself) then it somehow feels wrong. Another fun way that technologies can build on pre-existing psychological abilities.