mu4e has the ability to hide duplicates, with the "V" key, but I see no way to delete the messages. I've tried tricks with marking messages in and out of the hide state, but nothing seems to work well. Searching the documentation and googling has turned up nothing.
As far as I know mu and by extension mu4e does not support this and I don't think it ever will because it does not match its design principles. Instead of providing tools to make it easier to organize your inboxes more easily it replaces organizing with searching.
There is some support for explicitly organizing mail and by saving searches you are effectively doing something similar. But the idea is that we receive so much mail that it has become inefficient to manually organize and vet our inboxes. Its not considered an issue that there might be duplicates, boring mail isn't deleted etc. Mu/mu4e is supposed to let us forget about these issues by providing good search.
There are duplicates in your sea of messages but that isn't considered an issue. Only that duplicates might be displayed is considered an issue. And for that there is
(setq mu4e-headers-skip-duplicates t).