Ninjask, as I have used it and as practically every other user has, should be used as a lead. Phazing isn't that common in leads. That is not to say that it is bad, far from it: if people used Ninjask more, phazing would become more common and what you said would be more accurate. Again, Nidoqueen is a late-game sweeper, which is certainly not the time of the battle when Ninjask is used.Ninjask is an okay Pokemon, but it's got a couple pretty major problems that stop it from really being effective. First and foremost, anything with a phazing move is completely shutting it down. Stuff like Rhydon, Steelix, even Mandibuzz can all stop it from successfully getting a pass off. Another pretty big issue that Ninjask has is that it can't stop Taunt, which means that stuff like Qwilfish and some Aggron can stop it from passing successfully. Finally, the pure offensive pressure from some pokemon in RU such as Nidoqueen can be enough to OHKO the receiver once Ninjask gets the pass off. Again, an alright Pokemon, but it's really just fine where it is given its flaws and the support required to use it effectively.
OHKOing Ninjask is a problem, but it can be circumvented by using Focus Sash. Swords Dance first turn, the opponent reduces you to 1 HP, you Speed Boost. Then Baton Pass into something that resists the opponent's attacks (Entei, I have found, is an astounding partner to Ninjask, as it can OHKO half the meta with Extremespeed, let alone Flare Blitz, after a SD boost).
Mandibuzz is so rare that it shouldn't be taken into account on its own when making a team.
What you have said is correct, but only applies to using Ninjask late on in the game. It also is why Ninjask is not worthy of an S Rank, only A or possibly upper B.