As Ian Agol mentioned in his comment, the OP's question can be thought of in terms of the Orbifold Theorem. There are two (contemporaneous and) independent proofs of the Orbifold Theorem:
Daryl Cooper, Craig D. Hodgson, and Steven P. Kerckhoff, MR 1778789 Three-dimensional orbifolds and cone-manifolds, ISBN: 4-931469-05-1. (The relevant background chapter is available here https://projecteuclid.org/download/pdf_1/euclid.msjm/1389985818)
Michel Boileau, Bernhard Leeb, and Joan Porti, MR 2178962 Geometrization of 3-dimensional orbifolds, Ann. of Math. (2) 162 (2005), no. 1, 195--290.
The background section of either paper seems to answer the OP's question. However, here is my attempt to present the necessary details:
Consider the warm up case, if the double branched cover $M_L$ of a link (embedded in $S^3$) $L$ is geometric (in the sense of admitting one the eight Thurston geometries), then $M$ double covers a geometric orbifold $Q$ which has underlying space $S^3$ and the singular locus has cone angle $\pi$ and is isotopic to $L$ (as an embedded link in $S^3$). This covers cases 3) and 4) of the OP's question. Good background for Case 3) is the work of Montesinos, especially his book Classical Tessellations and Three-Manifolds.
Otherwise, there is an obstruction to geometrization. For closed, orientable 3-manifolds, the obstructions to geometrization are embedded $S^2$ which do not bound $B^3$'s and incompressible $T^2$. As a result of the two papers cited above, the obstructions to (closed) orbifold geometrization are more or less analogous.
First, we need to discuss bad 2-orbifolds of $Q$, i.e. 2-orbifolds which have underlying space $S^2$ transversely intersect the singular locus $Q$ in exactly one point. This is equivalent to such a 2-orbifold not having a manifold cover (see for example Chapter 13 of Thurston's notes).
For the rest of the argument we will restrict to the case of an orbifold $Q$ with underlying space $S^3$ and having a singular locus a link $L$ labeled only by cone angle $\pi$.
EDIT: the paragraph below originally forgot to consider split links. Thanks to the OP for pointing this out.
1) In this context $Q$ is reducible if it contains a) an embedded bad sub-2-orbifold, b) an embedded 2-sphere which does not bound a 3-ball, or c) an embedded 2-fold orientable quotient of 2-sphere which does not bound the quotient obtained by rotating a 3-ball along an unknotted arc. This perspective more naturally generalizes to arguments of the above two papers. In the case of the question, we see that $Q$ will contain an embedded 2-sphere which does not bound a 3-ball if and only if $L$ is split and $Q$ will contain an embedded 2-fold orientable quotient of 2-sphere as in case c) if and only if $L$ is not prime. Furthermore, if $L$ is split or non-prime link, then each piece of a prime decomposition of the link $L$ will correspond to a prime decomposition of the orbifold $Q$ and a prime decomposition of $M_L$. (The general case involves consideration of more 2-orbifold quotients of $S^2$.) So the orbifold version of reducible involves both contains an essential 2-sphere quotient and bad 2-orbifolds.
2) The final case to consider is if $Q$ is irreducible but not geometric. In this case, $Q$ is the orbifold equivalent of being toroidal. The second reference uses the term toric for this case, but we will follow the first reference an say that an orbifold $Q$ is orbifold-atoroidal. Before the precise definition, notice that a torus $T^2$ has a unique orientable 2-fold quotient $S^2(2,2,2,2)$ (a 2-sphere with four cone points of order 2, sometimes called a pillow case). A rational tangle in a 3-ball can be obtained by taking two embedded unknotted arcs in 3-ball and then twisting along their boundaries. Assuming $Q$ irreducible, an embedded $T^2$ is incompressible if it does not bound solid torus to one side. In an irreducible 3-orbifold, an embedded $S^2(2,2,2,2)$ is incompressible if it does not bound a rational tangle to one side. If $Q$ contains an incompressible $T^2$ or $S^2(2,2,2,2)$, then we say $Q$ is orbifold-toroidal and otherwise $Q$ is orbifold-atoroidal. (The more general definition of orbifold-atoroidal involves considering more general quotients of $T^2$.) For the specific instance above, $Q$ is orbifold-toroidal if $L$ is a satellite link or if $L$ contains an essential Conway sphere, which is really just a concise restatement of the above paragraph. The decomposition of $L$ along satellite tori and essential Conway spheres leads to a JSJ-decomposition of $M_L$.
