Every package denotes in its META file only the list of direct ancestors. The theoretical model of the dependency relation is a directed acyclic graph (DAG), with the packages as vertices and edges from packages to their direct ancestors. The graph must be acyclic because OCaml does not allow cyclic dependencies between modules.
What happens if you query something like
ocamlfind query -recursive p1 p2 ... pN
is that the named packages p1 to pN are marked in the graph, and that repeatedly all direct ancestors of marked packages are marked, too, until there is not any marked package remaining with an unmarked ancestor. All marked packages are then printed in topological order. This simply means that for the printed packages p1 to pM holds that if pI is printed before pJ then pI is a (possibly indirect) ancestor of pJ.
The topological order plays a role when the link command is constructed by "ocamlfind ocamlc", as Ocaml requires that archives must be linked in topological order. For example, the link statement
ocamlfind ocamlc -o another -package q -linkpkg another.ml
must be turned into the effective command
ocamlc -o another [...more options...] p.cma q.cma another.ml
ocamlc -o another [...more options...] q.cma p.cma another.ml
because there are references from q.cma to p.cma.
In C, there is a similar requirement when linking static archives. The linker backend ld wants the archives in reversed topological order, i.e. the deepest ancestor must come last in the list of linked archives. Because of this, the additional linker options specified in the "linkopts" variable are passed in reversed order to the underlying linker. This means that you can refer to C libraries of ancestor packages of p in C libraries provided in p.
Note that most operating systems do not require any specific order for dynamically linked C libraries (the exception is, surprise!, AIX).