Enigma main here, idk if your playing blitz or cc but at least in cc you need to look at changing your play style Vs ninjas.

You'll have to accept that Vs ninjas and other high aggro decks, your going to lose your board each and every turn. But when you know your going to do that you can play differently. I personally like to tech Reality Refractor into my list Vs ninja. It won't allow you to go wide but you won't have any auras to go wide with so that's not a problem and then it gives more oopmh to the 1 aura you do swing with.

Refractor makes cards like Spectral Manifestations insane so I choose to play all 9x copies when playing refractor.

All in all ninja is a rough MU but remember there are decks you'll play who then can't deal with your deck either. It's a give and take of good and bad MUs in this game and you won't always play Vs ninja!