a trick to fight pos1 shisui with lower or higher initiative than you is to use ninja with reflect.

Fire main
kurenai
One of the pain

You either wait for their shisui to fire first if they have pos1 init over you, or you fire first to cc 1 of their other ninja. Their shisui will not cast mastery if you have reflect active. But to completely counter root lm team with shisui+itachi, you kind of need some buff removal ninja as well or else that double hit from shisui and itachi will wear your team down fast.