Folders aren't for filing emails after you've read them. Used well, they're for filing incoming messages automatically. I have a heavily email-driven workflow, and I am active on dozens of mailing lists. My email servers filter incoming messages and deliver them directly into folders based on which list they're coming into. Another filter has a list of commerce-associated domains that get filed into folders based on which accounts they're associated with. As a result, the only mail that hits my inbox proper is mail from friends and family (plus the occasional not-filtered-yet work/list mail). Everything else lands in folders, and I prioritize opening those folders and dealing with those messages.

As you mentioned, once a message is 'consumed,' it just gets archived. But the folder system (combined with sieve filters) is what makes dealing with a ton of incoming email extremely pleasant.