When the game is set to automatically handle events and the other player has zero creatures to block with, the ninjitsu animation will play on cards able to use the ability, however the game does not pauses, and immediately progresses from attacking to damage. The same also happens for cards with sneak. This only happens when the opponent has zero creatures on their side of the board. If there's a creature that has 'can not block', the game pauses as it should.

The game should be handling this exactly the same way it does when instant and flash abilities are available. I think that there's a check that's not being performed correctly when the game analyses blocked/not blocked attackers in this case.

Setting the game to manual mode allows ninjitsu and sneak to operate as intended when the opponent has no creatures.