Funny. Hibiki like En also has several private type rooms which are very accommodating to families.
We've never had issues with our child on the four times we've been in Japan when she was 9, 7, 5 and 3.
Sure, we rarely see any local children in the centre of Tokyo at 6pm for dinner, but never a problem.
Thankfully that the more and more smoking is restricted indoors, it will get even easier.
I find that going right when the place open is best and make sure you make a reservation so they know there will be a child in advance.