I have a couple of Japanese maple volunteers from my yard that have been in my grow garden for a couple of seasons. When should I think about removing the tap root?
As soon as you can without compromising the health of the tree. I didn't look at your location but if they haven't woken up yet you could do it now. It goes without saying to make sure there are enough feeder roots to sustain the tree. The longer you wait (in terms of years) the more of a pain it will be. If they have already leafed out, just do it next spring before they leaf out again.
When you do, be sure to spread the roots radially, and then plant them over a tile or something flat to keep the roots running out and not down. Start that nebari out right the first time!
I've grown many JMs from seed and the tap root has never been an issue. So, I wouldn't worry about it. When it comes time to put in a bonsai tray, you're going to end up taking a saw to the root mass anyway.