Files are categorized by folders. Folder may be a structure folder e.g. obj/ item/ weapon/ gun/; or a separation folder e.g. onyx_sprites_2019/ jungle_2014/ etc.
No specific structure is enforced, but please put some effort into keeping things organized and discoverable.
Note that optional doesn't mean you have to. If you're short on time, tired, or just lazy, as we all sometimes are, feel free to just dump the files somewhere and move on. Either future you or someone else will eventually get to them and clean up.
My personal preference is to put a small readme.md file alongside the sprites that are being stored, explaining what this is, when it was, possibly why it was removed, and any other historical details that might be relevant or insteresting to guests of this archive. A commit hash/link of when the file was added might be useful to others, this allows people to explore the context around these sprites, the code that the sprites were related to and just get a glimpse of the era when something was drawn.
Since .dmi files are a niche file format, there is no easy way to view them through the browser or file explorer. Having a preview allows others to preview the contents without having to download each .dmi separately and open them in the DreamMaker.
As such, you can include a preview image of the sprites in the folder. Put your image into the same folder as your readme and use  markdown format to embed your preview into the readme.
If you're adding multiple .dmi files and want to make a preview, no need to make a preview image for every file separately. Just open Paint or whatever and slap some screenshots of the DreamMaker/dmi-editor windows together to at least capture the essense of the sprites, that's good enough. If anyone will be interested in more details, they'll download the files and will figure it out on their own.
This is historical stuff from hundreds of contributors over the last 20+ years and probably multiple codebases, what do you mean license? ._.
Jokes aside, nowadays (2024) SS13 is mostly using AGPLv3, so basically keep stuff open source.
(gnu.org is down quite often, but you'll manage to find the license text if you care about this stuff).
Some codebases use Creative Commons 3.0 BY-SA or Creative Commons 3.0 BY-NC-SA for their assets (and apparently code too in goonstation's case?), so basically give credit where it's due, don't try to sell these sprites (lol), and distribute under the same Creative Commons license if the sprite is licensed under it.
If you know what license the sprite/set of sprites is under, want to explicitly specify the license for your files, or know that files use some unique license that is not mentioned above, feel free to add that to the respective readme.md. Otherwise... well, don't be a space asshole.