I’m not sure it’s counter-intuitive as this stuff is all abstract, but it is inconsistent with object axes showing at the origin point. If I recall correctly, Maya puts their bone axes as you suggest (been a while since I’ve used it), and I don’t know how 3DS handles it, but if your “intuition” developed from using other software, that’s a different issue.
As you note, a practical consideration may have been that, since the axes shown are all positive, the y-axis would be obscured by the bone display. Then again, the next bone may be in the way, so who knows? As was alluded to in other comments, the decision was made long ago, and there probably wasn’t a great deal of R&D put into the choice.