The AxiDraw’s EBB control board has a (very short) command queue, the one-level deep FIFO. So long as each command arrives before the last move finishes, you’ll be in good shape. (You can query if a move is done, or if the FIFO is full if you need to, but generally it works well enough to calculate your moves on a rough schedule, and let your computer+USB do the heavy lifting of the scheduling.)
On the two questions:
(1) The processing time is negligible compared to the typical motion time, so no worries there.
(2) The AxiDraw software does use the SM command to execute its moves.