No it will not affect the airflow inside the case. You point them fans towards the back, that way the warm air gets exhausted out through the back fan. Also with 2 fans for push-pull you can use low rpm low noise fans. That's the beauty of using push-pull for it gives better airflow and allows using two low rpm fans.
Actually, due to fin density, theyre quite different coolers. Ultra-120 will definetly outperform and benefit a lot from high CFM fans, but if youre looking for silent over performance the Ninja will be a better choice.