Nagato wins. CST is not necessary seeing that unhealthy Nagato's normal Shinra Tensei has
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much force, meaning a healthy Nagato's ST would be significantly stronger, and a healthy Nagato's boss-toad sized ST even more powerful than that. Thus, Itachi and Sasuke would have to maintain a V3 Susano'o or higher throughout the match, otherwise Sasuke dies to a boss-sized ST which neither he nor Itachi can anticipate. Even V3 Susano'o would likely get destroyed seeing what Danzo's much weaker Fuuton did to Sasuke's.
Nagato's chameleon summon can still come into play here, seeing that Itachi failed to detect it when Nagato began his ambush on him, Bee and Naruto. As a result, he can keep the bros busy with destroying his other summons (and attempting to destroy Cerberus until they realise Amaterasu is needed to defeat it) then hide in the chameleon for surprise ST/BT + chakra rods + Soul Rip. Or have it ambush Sasuke/Itachi by itself by restraining them with its tail, giving him an opening for BT + chakra rods + Soul Rip.
As per usual, Preta Path makes their ranged attacks useless bar kunai/shuriken/Kirin, and Nagato's sensing abilities make it easy for him to anticipate Amaterasu and clones. Having Deva Path's speed feats also means that taking advantage of his 5 second cooldown becomes much harder, seeing that Deva dodged Rasenshuriken twice (
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), and was fast enough to outrun 6T Kyuubi Naruto. Thus, even if Nagato can't put them down with normal STs and Asura Path cannons, he can most definitely survive long enough to use CST or CT.
Also, lol at whoever said that Susano'o arrows and Magatamas would destroy CT when both of their destructive feats pale in comparison to KCM Rasenshuriken, which pales in comparison to Bee's Bijuudama. CT tanks them both, and would most likely have gathered a large amount of rocks around itself anyways seeing that they have no intel on it, leaving Sasuke dead and Itachi crushed, with Nagato free to rip out his soul when he ends the technique.