first, she has an ability to manipulate "time", the specifics of what "time" is is not given, it is said, i think that she can slow down things, accelerate them, and make things from other times (timelines ?) come into hers.
the first problem : in forbidden scrollery, sakuya says to reimu that what she calls "stopping time", is just moving at incredible speeds.
first option, reimu is kinda accusing sakuya of kidnapping, and because she can stop time, sakuya is suspect, so sakuya could lie to look less suspect : this dosen't really make sense, since just afterwards, sakuya tells reimu to be suspicious of byakuren since she can move extremely fast : she wouldn't say that she can't kidnap kosuzu because she can only move at high speed and afterwards call someone suspect because she can move fast.
another option, the one i tend to think is the most belivable one, is that it is a mark of weakness in the ability of sakuya : she dosen't say that she can't stop time, she says that she can't stop time to kidnap kosuzu in that situation, making her "stopping time" ability look suddenly different from what we could think at first glance.
here is a theory of mine : sakuya can't stop time, but she can stop one's time, meaning that, in a village situation, she would have to stop everyone in the village in order to "stop time", we don't know how limited her ability is but i think she can't do that, instead, if she was faster, faster than light as WaHH implies, it would be as if she stopped time : sakuya would have so said "in this situation, i can not stop time, but what you would call stopping time, if i did, would be moving fast instead of stopping people".
my take on how her ability generaly works : it would be somehow alike remillia's ability to manipulate fate : the ability to manipulate one's time's worth.
to put it simply : imagine a man going up stairs : in five seconds, he will be going up four steps. sakuya could manipulate the worth of said five seconds : in five seconds, the man will be going one step. but as she changes one's entire time's worth, non only will they be going up less stairs, they will be breathing less, blinking less, ect... one will perform less actions for the same amount of time : their fate has been altered. she could make her own time worth more : in five seconds, instead of four steps, she will be doing seventy steps, going at insane speeds.
i think that logically, her ability would be limited to how much fate she can alter, meaning she can stop dust for a longer period of time than she can stop the watatsugi sisters, making sometimes stopping one's actions easier for "stopping time" and other times increaing her time's worth easier to "stop time".
also, if she stop someone, their actions are totaly inexistant, meaning : they don't exist anymore. it would explain why she won't just stop time and immediatly kill you, since you don't exist, the same thing applies to SWR for her knifes : stting still in the air, not able to be touched.
fell free to tell everything you think is wrong about what i said, that's the reason why i wrote it in the first place.