Just snip the fuel line in two and install a flow gauge in there. If hydrogen works, it should show up as slightly less fuel needed to push the engine against a brake dyno held at a certain speed.
I've talked to many hydrogen proponents, and the only ones who have any halfway sensible numbers to show are those using aftermarket engine management to "tweak" the engine to "optimize" running on hydrogen. The challenge is to show that the engine can't work at the "tweaked" settings without hydrogen boost, and that the fuel savings aren't simply due to running the engine leaner... which can be done in most cases on typically conservative factory fuel maps.
All the doubletalk in the world can't cover up the fact that there is no dyno evidence and no scientific evidence for "HHO". On the other hand, there's plenty of evidence for meth-injection and water-injection (though water-injection benefits in terms of economy aren't really that big), which don't rely on hocus pocus to work.
I've got a dyno I can borrow, as well as AFR sensors and an OBD reader that can be hooked up for dyno-sessions. And I've got a car equipped with a stable aftermarket EMS for a test bed.
Every time I hear one of these outlandish claims locally (HHO, fuel line magnets, magic fuel additives), I tell them: Pay me for the dyno-time, and we'll test it. If your numbers work out, then I'll publish the results.
So far, no takers. Big surprise. Well... some of the additives do work, a little... but not as effectively as simply buying higher octane gas...