This commander deck is not super competitive, and isn't aimed at the cEDH crowd. This is an "affordable" or less than $100 deck, half of which came out of my collection of the past 2 years. This deck focuses more on the tribal synergies of the ninjas and clearing the way with primarily bounce and repeated Enters The Battlefield (ETB) triggers to make sure we all get to value town as soon as possible. In addition, some top of the deck manipulation is in the deck, mainly through cantrips and draw spells like Ponder and Brainstorm, meaning Yuriko, the Tiger's Shadow does get to hit better targets than some, but the average Converted Mana Cost (CMC) of the cards in this list is not split between super-low aggro/tempo Ninjitsu enablers and high CMC Yuriko, the Tiger's Shadow payoffs. 

This deck is actually constructed in my go-to box that has a Standard, Pioneer, and Commander deck filled with all Dimir decks. (I'm a Grixis kind of guy.) So some omissions listed in the Maybeboard area of this deck are missing because they're in other decks or possible upgrades once more hobby budget becomes available. 

The plan is the same as any other Yuriko deck - get the tempo and bounce creatures onto the board each turn so you can Ninjitsu something unblocked. I focused on having enough Ninjas that do more things each turn so I have options. Use unblockables and evasive creatures to land Ninja hits.

There's no counter magic in this list, but it would be recommended as the main source of interaction outside of all the bounce present in the deck. Most of the high CMC spells aren't planning on being cast for their non-Ninjitsu costs, but mana and artifact ramp are still very important because you should be re-casting your creatures and ninjas as often as possible to get the ETB's, attack, and player damage triggers. So card draw and ramp are important like any other Commander deck.

Some of the blink or bounce effects should be used on your own stuff to ensure they stay protected from removal or wraths. Do NOT worry about paying Yuriko's commander tax, as you should be Ninjitsu'ing her instead of paying the tax. 

Graveyard hate isn't a big problem for you, as nothing is irreplaceable in this list with a lot of redundancy, so Ashiok and Tormod's Crypt are there to hate on other people's inevitable graveyard shenanigans. 

Remember, the damage done by your commander is unlikely to kill anyone from combat so making contact isn't as important - the attack reveal triggers will do that and the damage in combat is gravy on top.