As far as I had heard, the flags were intended really as a promotional tool for Gamescom, FD showed off some pics, and people then wanted them.
So they obliged for a limited time.
No idea if they will ever be back, or if we'll see any on other ships.
I predict that skins will move beyond simple the apparent fixed texture paint-jobs at some point and become something more configurable as well as become more alive as they age and stuff, like we've seen in the recent newsletter.