there should be two levels of "deprecation", one for mods like this that are no longer actively maintained by the author but still work perfectly fine (probably until 0.17 breaks almost all mods) and one for mods that no longer work, are buggy, or are no longer needed because their functionality is now available in vanilla or in other mods.
as i have been told, the portal api won't list deprecated mods unless you ask it for the exact name of the mod. thus not only the really old/buggy mods can't be automatically found and listed, but also those "still working but not maintained" mods. this applies eg for mod-managers and other utilities (like "ModMyFactory").
there are people who use older versions of factorio (either older sub-versions of the current version, or really old versions like 0.12 or 0.13) and who thus need old versions of mods (including those which are deprecated because their functionality is now included in vanilla). with the current handling of deprecated mods, it's difficult to find such mods automatically in a mod-manager.