The most obvious reason is when debugging with something like diff deterministic behaviour eliminates spurious changes. Also having a deterministic and well understood ordering rule eliminates any concern that order might matter, and that a bug or whatnot was due to a different order (regardless of whether such a concern actually makes sense.) also sorting output lists makes them more readable. I don't know how well tested Automake is but I would assume deterministic hash order would help there too.
Also note that Prior to hash randomization the key order would have been consistent between multiple runs. Thus when randomization was introduced the behaviour of Automake changed and effectively regressed. Sorting keys effectively restores the original behaviour.
Cheers
Yves