Regular hierarchies should be more prevalent
I have made the same observations as you, and I think it is sad that most apps are limited to runway and 10,000 ft. There seems to be such a simple and otherwise common solution. They could simply implement a "folder" structure in the left panel, just like Windows Explorer, Google Drive and many other apps.
I think they should still call these elements "projects" instead of "folders", because that is how they would probably initially be used by most users, but users would be able to use them as AoF containers or Goal containers or whatever - group and map their tasks as high as they want. Or conversely, break larger projects down into subprojects.
As far as workarounds, yes, like @vbamton says, you can using naming conventions, and or/you can use tags for filtering purposes. This will help to some extent, but you will still have a gigantic left menu. Personally I use a bit of both, and what I do in addition is something that boils down to a "manual" workaround:
I refuse to have a mile-long list of 10k projects in my left menu. Essentially those are still just "tasks" in the general English sense, and I want a better overview than that. What I have there instead is a bunch of AoFs and a bunch of really large projects and 30 k goals. This gives me the overview I want, but it also means I have only the task level and comment level left to play with for 10 k projects and tasks. That means I would drown in tasks in each of these folders, so I use the task level only for those tasks that are Next or very near etc, but for the more distant (not-yet-possible) things I use the tasks as project containers and list the individual actions and subprojects in the notes, and then manually convert these to tasks (and apply tags etc) when the time is ripe. Clunky, yes, but my personality does not allow me to have long lists either in the left menu or in individual folders - if I cannot grasp the list mentally I go nuts.
As @mcogilvie says, Todoist is an excellent choice if you want hierarchies, or you can use an outliner such as Workflowy. Unfortunately, neither of these have equally handy features for listing/filtering/viewing as those that call themselves GTD apps. Personally I use Nirvana, and am also looking at Doit and Zendone and others.