I won't be too worried. Imo, since the collection scrolls seems to closely follow the game storyline, there should be 2 more scrolls for Five Kages Conference and Great Ninja War. Perhaps the GNW ninjas will be on the later ones?

I suppose you just join a new server ornew to the game, which is why you haven't had the chance to collect that many Kureinai/Hinata frags yet? But really, why bother? Sweeping should still give you their frags for breakthrough or upgrade, albeit less then before (which will slow your progress, on this I empathize). And even if you just want frags for refinement, go for Kabuto, he's 2000 points a day with relative ease.

Be patient, maybe they'll add those ninja back as redeemable. Maybe.