Exactly the point I seem to have failed to make clearly. Yes - exactly, which spark are you wasting? The combustion stroke? Or the wasted spark? Let your DDFF (Double D Flip Flop) miss a single clock signal and your timing will be 180˚ off and your engine will stall out.The major question is how will you see which rotation is the one to inhibit the plug firing on?
As has been said already, you need to sense the exact position of the cam shaft in order to eliminate the wasted spark. That is to ground the ignition during that wasted spark. Whether you can accomplish that with a second set of points INSIDE the crank case or not - you have to get that signal outside the case. Only then can you cut the wasted spark. But you're still left with the problem of timing for firing a hydrogen charge. But lets suppose you already have figured out how to change the timing so the spark occurs at TDC (Top Dead Center): What are you going to do to prevent hydrogen from gathering inside the crank case? Or backfire through the intake manifold? I would think you would have to put heavier springs on the valves to ensure they are absolutely closed when they're supposed to be. You will also have to make sure the valve seats are perfect. Or near perfect. But there's still the natural blow-by that occurs because piston rings do not seal 100%. They have to be gapped so when they heat up and expand they don't jam the cylinder. But if they don't close up all the way then you have blow-by. Especially when the piston, cylinder and rings are cold. All these problems should have been already considered by a true engineer. Someone questioned whether you're truly an engineer. Well, I'm not an engineer. And yet I have considered these issues. I'm also NOT a small engines guy. I can fix them. I can modify them. So I can understand the issues that need to be addressed. That's why I said my opinion is that you best leave well enough alone. Otherwise you're potentially going to be surprised at how much can go wrong with an internal combustion engine.
I wish you all the best. But you're still going to have to use some kind of points or contact internally on one of the two cam lobes. Without looking back, I think this may be an over head cam setup. If so - the problem becomes easier, but it's still not fool proof. Oil, especially dirty oil, can be conductive. Buildup on the points can cause the entire shutdown of the engine. But an engineer should already know all this stuff.
Good luck.