Very good question. I primarily arrange the roots horizontally, but I don’t know that the arrangement is the key element. If there are a lot of roots and they spread out radially that will be enough to create the flare or taper we look for in smaller trees.
The main thing I’ve learned is that for shohin, more than for larger pines, it’s important to cut back the larger roots as they develop and encourage as many fine roots as possible that emerge from the base of the trunk, not unlike what we’d expect on a trident maple. As you noted, there’s little room between the base of the trunk and the edge of the pot on shohin so the transition from trunk to fine roots happens quickly.
I’ll look to post more on how I work on this going forward, but in the meantime, here are two articles that show why letting horizontal roots get bigger and fuse together over time is counterproductive.