You don't seem to understand how certain speed amp works like Shishi sonson. Thought-based abilities have a limit to what they can do, the name is pretty much self-explanatory it requires you to think to active it's effect/ability, but the thing here is Shishi sonson blitzes.
For example, you have a Thought-based ability (let's say you have some sort of barrier), but someone jumps out of a bush and shoots at you from behind without any hesitation, and the last thing you sees is a person pointing a gun at you who already pulled the trigger, so does that mean you had the time to think in order to activate the barrier to protect yourself from the bullet that's massively faster than your brain can process, in short the imaginary you is dead, because the bullet utterly blitzed you, even in a real life battle you wouldn't even get the chance to think before getting killed by two professional soldiers.
So in other words, Zoro uses Shishi sonson and blitzes Musashi before she got the time to think. In order to activate her Fate hax (that's Thought-based) she need to think or reacting to Zoro's Shishi sonson before it hits her, but as explained above it will hit her.