When updating a published ship on Steam, the description in the text box is not populated with the description on the workshop entry. So if you edit the description of your ship using the Steam GUI (as I am sure most people will because the text box in game is woefully inadequate, lacking the ability to copy, paste, select, or scroll the cursor left or right...), updating the Steam entry with any changes you made in game will wipe out your entry's description if you are not careful.
As well, if you change the title of your workshop entry in the Steam GUI, things will work fine until you exit the game and start it up again, at which point the link between a ship file and its published counterpart on the workshop is lost. Re-publishing creates a new, duplicate entry.
Also, I kind of wish the workshop used my own heraldry for it's generated images, especially since I picked the paint scheme specifically to match the roundels and emblems that I use.
I'm surprised that Steam doesn't offer anything like a UID for workshop entries, but I guess it's not too big a deal. #1 is the more problematic issue.