You definitely want to be using Leftovers on Ninjask. The 6% recovery allows you get off more Substitutes and with Protect makes it very effective to stall for Speed boosts. The amount of defensive investment means that Focus Sash is not really needed to set up Swords Dances anyways. Having Leftovers with Protect gives you multiple chances to boost up as well as is much more reliably for teams that depend on Ninjask passing speed. (Full Baton Pass and NinWak combo come to mind) Having Substitute in the set already ruins the Focus Sash, so there really isn't any reason to use it.
Other than that Ninjask is a decent Pokemon to be leading with but I would not recommend it as something that should be leading all the time. Golem is starting to get more traction again and it absolutely destroys Ninjask with Rock Blast. Even Piloswine can beat it easily with Icicle Spear + Ice Shard. This is pretty much the reason that teams incorporating Ninjask have narrowed themselves down to NinWak or full BP. At least with Marowak you have an effective way of taking down Golem and a good recipient of the Speed boosts.