Activating Yuriko's commander ninjutsu ability isn't the same as casting Yuriko as a spell. You won't have to pay the commander tax to activate that ability, and activating that ability won't increase the commander tax to pay later.

If a card in a player's library has in its mana cost, X is considered to be 0.

Although the ninjutsu ability has the creature enter the battlefield attacking, it was never declared as an attacking creature (for the purposes of abilities that trigger whenever a creature attacks, for example).

Commander ninjutsu is a variant of ninjutsu that can be activated from the command zone as well as from your hand. Just as with regular ninjutsu, the Ninja enters attacking the player or planeswalker that the returned creature was attacking.