[jbn]

Hierarchical structure is one way we humans deal with scale, so yes.

To extract structure from large systems, one uses the design structure matrix (DSM). Look at the Eppinger book.

In software, dependencies are often expressed (in code, in Makefiles, in maven pom files, etc..) so the structure tends to be hierarchical and not have loops (i.e. the dependency graph forms a tree), otherwise it's not buildable from scratch...