In this case, your other 2 <Water Beast>SIGNI remain on the field, and Shironakuji loses -6000 power twice. If Shironakuji's power reaches 0 or less in this way, it is banished instead of being removed by your opponent's effect.  If Shironakuji had 13000 or more power, it is removed from the field by the opponent's effect.
If you have 2 Shironakuji, Water Phantoms on your field and your opponent uses Late Bloomer or other cards which will banish both Shironakuji, you may use both Shironakuji's [Constant] to protect the other. In this case, both Shironakuji will lose -6000 power.