I don't use Joplin for the aforementioned reasons earlier, but they should at least let you customize the "media folder".

The embedded media is already referenced using relatively standard markdown syntax in a respective MD note, e.g.:

    ![image info](./pictures/image.png)

Since apps such as Logseq and Obsidian work with your existing notes, they avoid this issue of massive file duplication and don't need to move the files at all.

EDIT: I just realized if you're talking about adding media onto a note through the notetaking application itself, take a look at what Typora does as a good example of how to handle it. It auto-creates a relative folder called "note_name.assets" and moves them to it. Obsidian OTOH lets you specify a "media" folder that exists for each subdirectory of your existing note structure.