An interesting proposal. First I want to warn you that I just finished an assignment that had me panning through Shakespearean literature, and since it's 3 AM, my choice of vocabulary may reflect that. But I digress.
My first instinct is to check PMiSS, since you know. This is what it has to say on her ability:
The ability to manipulate death means just as it says, the ability to kill someone with no resistance.
Once they're dead, she would be able to control their spirit as well.
Nothing good can come out of challenging her.
This reinforces my first conclusion (which I have yet to present), which is that manipulation of death is either very similar to or possibly inclusive of 'manipulation of THE dead.' Since we know she can control the spirits of the dead, I find it wouldn't be such a stretch to say she can control other undead as well.
This immediately made me wonder, are touhou vampires canonically undead or just a type of Youkai? If the former, theoretically Yuyuko would be able to manipulate them as other undead. If not...she should be able to kill them and then manipulate their spirits I suppose?
Regardless, there is no specification in PMiSS as to whether being able to manipulate 'spirits' of the dead extends to manipulating the 'bodies' of the dead, so I can't even say definitively whether I think Yuyuko would be able to manipulate someone like Yoshika.
I
suspect that her ability only extends as far as manipulating spirits of the deceased, not undead themselves, but I have no evidence to really back that claim up.
As far as the ability to kill concepts, my instinct is no, but it's hard to say that when presented with the 'fly out of reality' comparison lol.
However I would argue as such: manipulation of death is a lot more specific than it sounds. 'Existing,' or 'being' is not sufficient to ascribe the term 'life' to something. As such, though a metaphorical 'death' may be possible for a concept or an object, its just that, a metaphor. To be able to invoke death in something, I would first argue that that thing must carry an attribute of 'life', which theoretical existences like 'fate,' the 'theory of relativity,' or indeed 'Gensokyo' don't have.
You could even flip that argument on its head, saying that since immortals like Kaguya and Mokou, are immune to Yuyuko's abilities by virtue of the fact they aren't
alive. Since they don't age, their bodies fundamentally cannot change, and they have no aspect of death, one could simply argue they are not alive in the same sense that humans or youkai are alive. Thus, it is perfectly logical that Yuyuko would have no control over them or their deaths.
Some evidence for assuming that we can define death by its complementary aspect, life, comes from Kaguya's PMiSS article:
As eternity refers to a world with no history, it is also a world where change is eternally unknown. No matter how much you may try to bring about change in such a world, it is futile in a world where time has essentially stopped.
What is important here is that the concept of 'eternity' is defined as 'a world with no history,' or 'a world where change is eternally unknown.' This demonstrates that 'eternity' itself is not its own concept, but is instead defined by its negative relationship with time. In the same vein, we can say death is defined by its negative relationship with life.
As far as Shiki vs Yukari and Co, the dictionary definition of the word Yukari uses (逆らえない) is 'to go against, oppose, disobey, defy.' So while you could technically argue that this means they'd lose to her in a fight, it seems more likely to me that they just don't want to stay and talk to her, and if she told them to, they wouldn't be able to disobey. Whether THAT means they couldn't beat her in a fight is a whole different can of worms :P