It seems that by using Japanese scoring that there would be races to capture dead stones which wouldn't get captured in regular Go. In normal go, you'd never waste moves to capture dead stones unless necessary. In some cases it would even create a new kind of three-color seki.
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$$| . O . O . . .
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- Click Here To Show Diagram Code
[go]$$B
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$$| S S . X . X .
$$| S S X X X X .
$$| . O X . X . .
$$| O O O X X . .
$$| . O . O . . .
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Neither black nor white can atari the four red stones in the corner, because it would allow the other to capture them and get the four points for prisoners. So would the red stones be alive? Also, red could play in one of the liberties to give the free points to the player to his left as a trade for some helpful play elsewhere on the board... Is table-talk permitted?
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$$| . S X . X . .
$$| S S X X X . .
$$| . O X . X . .
$$| O O O X X . .
$$| . O . O . . .
$$| O O O O . . .
$$| . . . . . . .
- Click Here To Show Diagram Code
[go]$$B
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$$| . S X . X . .
$$| S S X X X . .
$$| . O X . X . .
$$| O O O X X . .
$$| . O . O . . .
$$| O O O O . . .
$$| . . . . . . .[/go]
And what about this? Black has no shared liberties with the stones in question and doesn't even have a legal move to atari them. But white still can't capture them.
And if suicide were permitted, could you self-capture your own dead stones for points? If area scoring were used, the stones would be just dead as normal. Maybe prisoners should count as negative points for the captured player instead of points for the capturing player. That would make area and territory scoring consistent.