Yojimbos chance of scoring a Zanmato is, as said, based on his comatibility with Yuna.

There are some way of raising his comp.

Summon him a lot.
Do NOT let him get KO'ed.
Have him kill lots of monsters.
The more Gil he recieves, the better compatibility.


The compatibility can get lowered too.

Let him get KO'ed.
He uses his Daigoro attack.
You pay him less than 1000 Gil.


So the higher compatibility, the better chance of him using Zanmato.
Having him in Overdrive also raises the chance of Zanmato.