How strong exactly is Super Shadow? Because if he's stronger than Sakuya by a large amount, this could be stompy.
On the other hand, if he's anywhere near her in terms of AP, this seems like a poor matchup for him. As far as AP, Sakuya is like 4 or 5 levels up the scaling totem pole from a character who can fire 50 Universes in a single attack (Doremy Sweet) while still limited by the Danmaku rules, and has what would be a very hard move to tank for even peak Super Shadow with his lack of Spirit Manip resistance: the fact that without Spell Card rules in play, there is absolutely nothing holding Sakuya back from making a literally undodgeable Danmaku barrage that would attack Shadow's very soul, weakening him while simultaneously buffing up Sakuya.
So that's question one: Can Sakuya's Danmaku hurt Super Shadow, and if so, would Super Shadow have any chance at dodging it or weakening its effects? I think the answer to that second half is a clear no with the lack of resistance to Soul Hax, but I can't say anything about the first half.
Question two is who's signature Space/Time hax is better. From what I see, Sakuya's control over space/time is stronger than Super Shadow's, or at least there are feats that she has that Super Shadow doesn't have without much of a vice-versa. With that in mind, I think Sakuya takes the "better spacetime hax" category, though I think there could be arguments to the contrary.
Question three follows from that: Shadow does have Resistance Negation on his profile, but is that strong enough to overcome Sakuya's space/time resistance? I can't say for sure, but I can say that purely on description, Eientei's existence as a place outside Time and Causality is similar to Sonic's White Space being a place where Time doesn't exist. So it does seem possible that Sakuya would be affected by the Super Shadow Time shenanigans.
Shadow does lose the Hax battle for certain in the supplementary category, at least as far as wincons go. None of his resistances do anything to stop Sakuya's most notable wincon of existence erasure, though a secondary wincon of aging Shadow to death does go out the window due to type 1 immortality.
To sum up my feelings, Sakuya's profile needs a lot of work, but even as it stands there are a couple paths to victory, assuming she can't hurt Shadow at all. If she can hurt Shadow, or at least drain Spirit with Danmaku, then I think this becomes a somewhat easy W for Sakuya considering the stat advantage would quickly flip and she would be simultaneously attacking an area he has no defense in.
I'm leaning Sakuya as is for a different, related reason: Shadow literally has a stated weakness of getting cocky and overconfident, and with that in mind is far more likely to play with his food long enough for Sakuya to pull out EE and end the fight with a blow that Shadow has no resistance against whatsoever. If he's not far enough ahead on AP to make that playing fatal then I think he gets erased before he goes for the killshot.