Don't know what you mean by "small" but assume 12x 12, 13, 14, 16?
There is really no advantage in this case -- although no real disadvantage either except it will be harder to keep the acoustic variables symmetrical unless the room is an actual square. Harder too to get speakers sufficiently apart but maintain decent distance to sidewalls. And of course you might find yourself sitting in one of the corners where bass could be boomy.
Standing waves generally won't be a problem either way because of the small room size. I think the biggest difference you may discover is that the diagonal arrangement will require almost complete acoustical (absorbent) treatment of all walls, which in an axial setup could be more discretionary.