It seems like the rates aren't as what it was initially assumed to be before the launch of the treasure. Now that the treasure is out its about as follows from the numerous reports and pulls that people have done:
Rares range from 1-4 x10 Pulls: Snake Kabuto, Kinkaku, Ginkaku, Mu
Super Rares rage from 11-15 x10 Pulls: Gengetsu, Rasa
Every x10 pull gives you the usual normal 2* ninjas such as GNW Hinata, GNW Sai, GNW Tamari, etc.
*PS I think Susano Itachi appears easier to get fragments here. But that's just me looking at someone do a 130 pull for Gengetsu which got him 5 SS Itachi Frags. So its just my own inference.
Just a reminder, they are all 2* ninjas, and if you pull dupes for the Rare and Super Rare, its 25 fragments instead of the usual 20 we see in other treasures. So technically, if you spend 250 Seal scrolls, you'll probably pull dupes and one of your Rare will probably be able to be 3*.
Whether the ninjas are better, I'll leave it for others to debate. As an f2p myself, I have no use or desire to use these ninjas, except to be a pokemon collector, so I'll just skip and pray to get someone from free pull.
Don't quote me on any of this. ;P