Unfortunately, you are mixing up two different stores. BHV (Bazaar de l'Hotel de Ville) is in the 4th arrondissement and has the hardware department in the basement of the store. It does have a small restaurant (on the sixth floor I believe, near the toy department), but does not have the views etc of La Samaritaine.

La Samaritaine (http://en.wikipedia.org/wiki/La_Samaritaine) is in the 1st arrondissement with the restaurant and view, but it has been closed for some years and not expected to reopen for several more.

As to the OP's question, I am not familiar with any restaurant catering in particular to children, except perhaps for some of the chains (such as Hippopotamus). I would definitely recommend lunch over dinner, however, as dinner tends to start around 8pm and gets really moving around 9pm. In fact, many restaurants do not open before 7 or 8pm for dinner. Also, breakfast isn't really a big thing in Paris, its mostly just a croissant and coffee.

Just doing a quick search on google, it does seem like there is a "baby brunch" on Sundays at "Justine" in Le Meridian hotel near Montparnasse. Although that is probably targeted at younger audiences than 12/13.