I had the same concern so I called Sea Swirl. They suggested 2 options.
1) replace the 90 degree elbow with a 45 degree elbow.
2) add a downward extension so that the elbow well below the surface.
My tank is very tall (37"), and I plan to mount the SeaSwirls in the front corners of the tank, so I will probably try the 45 degree elbow so as to sweep the waterflow across the front of the reef. If I don't like the flow path, then I may try the extendion idea. I suppose you could also include 1 or 2 tees so that you have multiple outlets at different heights.
BTW, the 1" SeaSwirls don't come with LockLine fittings because they don't make them large enough. Of course, if you used multiple outlets, then you could use the LockLine