One way of indicating in a 3d mathematical diagram that one line is passing in front of another is to omit a small part of the line passing behind. A very specialized version of this is implemented in the syzygy module. In the code below, I provide a function drawUnder (defined in the module underpath) that simulates this effect for general 3d diagrams (as long as no surfaces are involved). It works by drawing a wide path3 the same color as the background that is directly behind the specified path3 relative to the camera. I have also included an example to illustrate the results.
I hope that you find this idea useful enough to incorporate the idea (with or without my code) into a future distribution of Asymptote.
For what it's worth, I have experimented some more with my code since posting this and have decided that it is definitely not ready to incorporate into a distribution, although I still think the basic idea is a good one and worth pursuing.