I've flown several flights directly over water (> 20flights), at significant distances from shore (up to 600m offshore) and had no signs of trouble with Skydio2. For me, it flies just the same as if it was over land.
I have not tried the beacon, but have been using the controller and flying either with Skydio2 app (on ipad) or with DroneDeploy (again on iPad) for pre-programmed autonomous survey missions (like mowing the lawn).
I haven't tried to fly super low to the water surface, but have done most of the flights either ~90m or ~30m AGL.
I don't think I would try the 'fly to spot' feature on the Skydio app where you push with your finger on the ipad where you want it to go... It seems possible that the real-time surface model might identify the bottom surface under water and try to fly there.