A lot of this is philosophy, which, per forum rules, doesn't really belong in these forums. But I'll try to just address the mathematical content of your post.
Stoney Pete said:
If we then use something like Von Neumann's defintion of an ordinal as a set that contains its predecessor, we could -- in a sense -- say that S = ω because S contains a predecessor which contains a predecessor etc.
First, von Neumann's construction of the ordinals is that a number is the set that contains
all of its predecessors, not just its immediate predecessor. This is a very important point, because the criterion "is a member of" gives a convenient and simple well-ordering. Thus, we can say that 2={0,1} is less than 3={0,1,2} because 2∈3. So the ordinal numbers are ordered (hence the name) by the inclusion relation. This wouldn't work if you defined, e.g., 1={0}, 2={1}={{0}}, etc., because now 0∉2, for example. You could potentially come up with another criterion for ordering, however.
Stoney Pete said:
If we take "→" to mean "contains as element" then we can write: v0→v1→v2→v3...etc. In a sense this means that v0=ω because v0 has infinitely many predecessors. But at the same time the graph comes full circle in v0 itself so that we would have to say that v0 is also ∅ or 0, the first predecessor!
v0 can't be the empty set, because it's not empty. The point of equating zero with the empty set is that by construction, it doesn't have a predecessor, so therefore it's the first member in the well-ordered set. A well-ordering is only possible if you single out a member that is the first in the set and say "this is the smallest," or "this is the Xest" for whatever property X you want to order.
Stoney Pete said:
So, in short, this is my question: Is it possible to design one hyperset that in its cyclical (= recursive?) structure can be seen as constructing or otherwise mirroring the natural number system?
I don't know for sure, but I doubt it. Non-well-founded sets (what you call hypersets) are infinitely recursive, so they have no bottom (or no first element, so to speak). Without a first element, you can't get a well-ordering. Since we generally think of well-ordering as a crucial property of natural numbers, I seriously doubt any system like this would work.