No, you can also upload ZIPs with plain images or sounds. It also support Dungeondraft packs.
Yes, Moulinette Cloud offers a lot of flexibility. You could make the assets of the month available to all your tiers and then change permissions to higher tiers only. You could also remove the pack entirely if you sell it otherwise (e.g. marketplace).
Read the help page available in the Moulinette module. Alternatively, you can read Moulinette documentation on GitHub.
Make sure that you have a 2-level structure (see documentation). Moulinette also lets you debug the process (enable it in the configuration). Open the console (F12) to see which folder is browsed and indexed by Moulinette. You could also try to test on a subset (e.g. 1 folder) to see if moulinette can index your assets.
If your Patreon account is linked with Moulinette but you don't see assets, try to unlink and re-authenticate.