I was clearly seeing these ships come from the command station. In both purple (AI 1) and green (AI 2). This was after clearing all ships from the system.
After the hack I had specifically gone on a quest to kill all bombards hoping to never have to see them in AI hands. It wasn't till about an hour later I found the second backup server. During this time I had noticed the reinforcements with bombards and was confused as to the status. After seeing the second one it took me about 15 minutes to realize the new one was purple, but I still saw green bombards spawning on purple worlds.
Only thing I can think of is since both AIs can reinforce any AI planet, in order to make it more straight forward and easy to understand for the player, the ban is for a certain AI's worlds, not for a certain AI's reinforcements. Otherwise a player might still see that ship type reinforcing every world and not notice which AI was actually reinforcing it.
Still, I feel that the tool tip is misleading. It makes no mention of the fact that each AI keeps separate backups, or that it affects any AI's ships spawned at that AI's worlds and not that AI's ability to reinforce anywhere.
I will see if I can get screenshots of this later when I pick back up the game. As for whether or not these ships existed before, I know those will remain. That is in fact mentioned in the tooltip.