8.8 cm Flak was just as often used against ground targets as it was used against air targets.
There were many cases in early war, where Germans specifically brought 8.8 cm Flak to the front, to deal with heavily armoured enemy tanks, because their regular AT guns were unable to penetrate the opposing tanks at longer ranges.
Tiger I's gun was also a repurposed 8.8. Flak gun.
So yes, these guns are more than capable of dealing with ground targets and it is historically accurate for them to do so.
Also, against what type of ship did you use it in the mission? :)