As those mentioned, placing a loop above the outlet prevents water coming down, but with a loop below the water line, they have similar results. Running the hose up and above the water outlet, without a loop would rely primarily on gravity to prevent water flowing down, as it has to travel upwards first. With a loop below the outlet, water that gets in would then have to travel upwards, against gravity, before it can come back down. That's quite a bit of momentum needed to do that and Im guessing you're seeing water collecting in that bottom section of that loop.
My main concern and advice if you do try raising loops higher in the bilge compartment is that the higher that tube is, it makes it harder for the bilge pump to actually push water out when it needs to. I don't know the specs of the bilge pump exactly, but I feel as though its strong enough to do what it needs to do but not the best, as most OEM parts. Yes, if you did raise the loops higher, it could do still pump water out, but it would add additional strain and wear it out faster.
I trailer my boat, so for me, this isn't a big deal. I too have waves push water in, but water enters from the anchor locker, people getting in out of the boat after being in the water, and other sources. When I get my boat out of the water, I unscrew that drain plug and let any residual water in the bilge get out.
If you are concerned about back flow, are you more concerned about water accumulating in the bilge or wear induced on the bilge pump itself?