I think something is getting mixed up in the explanation here. The "U-tubes" you are talking about drilling are the ones for the RETURN from the sump over the back wall of the tank. They need to be drilled (or very close to the surface) to minimize the amount of backsiphon that occurs when the return pump goes off. The check valves will always fail eventually. Even if they are taken off and cleaned weekly there is still the chance that a tiny snail or starfish could be inside the valve as it tries to close and props it open just enough to drain the contents of the display onto the floor.
The U-tube that you are worried about restarting is for a device called a "DUAL overflow". The reason it is called a DUAL overflow (everyone just calls them overflow boxes) is because they flow over (through the U-tube) from the main tank to the outside box and then once the outside box fills enough, the water overflows down the standpipe into the sump.
The water level in the display tank will drop until it reaches the bottom of the slots in the INTERNAL overflow box then it cannot enter the overflow any longer. The water will remain in the U-tube and internal box even if there is no movement of water using the same principals as when you put a glass under water and then lift it out bottom first the water stays in the glass until you break the surface with the rim. Even if you drained the entire tank at this point the siphon is still there and there is water in both the internal and external boxes to keep the ends of the U-tube submerged.
When the standpipe breaks the surface of the water in the external box the water will stop flowing down to the sump.
Then when power is restored the water level in the display will rise until it flows over the rim of the overflow box and becomes higher than the water outside the tank in the back overflow box. Then, because of gravity, it will flow out to the back overflow box and fill it until the level reaches the top of the standpipe and begins to flow down to the sump again.
They are really safe and THOUSANDS of people have used overflow boxes for years without any problems. The problem is the if you somehow lose siphon in the U-tube then the water will NOT begin to flow over the back and the display will overflow. if you have bubbles flowing through the U-tube and they accumulate in the top of the tube over time they will form a large air pocket in the top and stop your siphon. This is why CPR uses the Aqualifter pump to constantly pull air out of their overflow tubes and prevent that problem.
When I used an overflow box I ran 2 totally seperate units so that if one completely failed the other could keep up until I found out and fixed the problem. Much the same way people use four 1.5" bulkheads when they could get all their flow through two. It is a question of "what are you willing to trust?"
I have no problem using a dual overflow but I prefer the cleaner design fewer chances for trouble gain by drilling the tank.
Here is a pic to help illustrate the DUAL overflow design.
Hope that helps,
-- Kevin