Okay, we all know that scorpion's wife and clan is massacred (at least storyline-wise), but I highly doubt that Quan Chi could kill an honorable and respected clan like the Shira Ryu. Here goes my idea:

ok you remember when Quan Chi escaped the netherealm with Shinnok? Well I believe that Quan Chi somehow hired the Shira Ryu and they helped him get Shinnok out of Hell. Now, here are the two theories on how they died:
1) Quan Chi and Shinnok left the clan in the netherealm and they died to the oni/omni killed them from there.

2) As they escaped the Netherealm, Shinnok and Quan Chi killed them off with the amulet's power.

Post you opinions