Probably, because it may be better not to have higher loss over longer sentences just because they are long. And according to Stanford CS224n lecture 8 NMT objective is mean cross-entropy.
Also, averaging over batch dimension is needed to have batch-invariant learning rate.
I talked to some friends who did machine translation and it seems that this choice (of not averating) is pretty arbitrary. However, it tends to give a bit better results for no obvious reason.