If there's no risk, then why ever bother playing the actual combat out?
Even those pirate ships may get lucky every once in a while. They do in the real battles, after all; they should do so in auto-battles.
I think the save-scumming issue is pretty moot. Save-scumming is an available choice for all combat outcomes in anything but Iron Mode.
So long as there isn't any realistic possibility of excessively lucky good dice rolls allowing players to get unreasonable results from repeated runs through an auto-battle, it's a non-problem, especially if, on average, it's worse than just fighting it out.
I really don't mind the concept of players doing a lot of auto-battles once they can build their own fleets and such, but at that point, trading losses with enemy fleets and returning to your base to repeat the process is a time tool (and may or may not save the player time) but it'll be largely at a net loss vs. manually fighting the battles.
In short, auto-battle should always be seen as a time-saver that costs ships and crew, never as a good alternative to fighting a battle manually. Otherwise once there's more to do, the game's merely about stacking your fleets to auto-kill X to get Y done, rather than mastering the core gameplay. It's almost that bad now; take a custom fleet with high-end ships and max out travel speeds so that you can catch small fry and watch the profits roll in.
I don't mind the idea of having other fleets around to help your personal fleet win fights, etc., but at the end of the day, it needs to be better to go do the twitch dance or all the game guides will merely be fleet-stacking guides and how to get the MacGuffins, which would be a real shame.