Why is it common for anime to lack surround sound?
Probably the only anime that I saw with 5.1 audio is Evangelion. However as you've pointed out, most(if not all) TV-aired anime in Japan are in stereo unless it got released into special BD/DVD.

This issue is also under budget constraints, etc. It's not budget-wise to apply one, just the same as what @Dmitri said about the average Japanese household.