Why can Naruto still use Rasenshuriken?
Naruto only used this jutsu one time in normal form (against Kakuzu, and got many side effects, like you said), the other times he was at Sage mode, at this state he didn't damage himself.

According to Naruto  Wiki:


  Naruto later improved the Rasenshuriken with Sage Mode. This allows
  him to throw it at his opponents, and removes the threat of damaging
  himself with the technique.