I'd say every file of an addon should be in a folder unique to that addon, documentation included. Crowding aside, also means stuff that shouldn't doesn't get overwritten. If anything, it makes managing files easier for the dev I think.
The zip thing just depends if you zip up all the individual addon folders or the folder containing them. I always open the zip and copy the folders myself, so to me it's irrelevant, but no extra effort in doing the former.