Well, the only reason I'm aware of to assume that they were "scrubbed clean" is if one has ascertained they were bioweapon plants. The failure to find any evidence of biological agents - once you've already concluded that they're bioweapon plants - leads to the assumption that they were scrubbed clean.
Circular argument, anyone?
It was said when the anouncements were first made of the trucks, that some sort of caustic material was used to wipe down interior surfaces, and on the outside, fresh paint applied. This would be an EXAMPLE of their having been scrubbed clean.
So you're admitting that if they had been scrubbed clean with, say, a caustic substance, that the only plausible use for them would be bioweapon plants?
It is assumed that they were scrubbed clean because no credible other use for the vehicle has been presented. The hydrogen excuse is not credible, despite the claims of the people in this article, for the reasons I describe just above.
So if you have these vehicles, and you can't think of a non-weapons use for the vehicles that makes sense, and the Iraqi's explanation for the use of the vehicles is shown to not be the case on the vehicles in hand, and you can't find any vehicles showing evidence of being used the way the Iraqis say they were used, where does that leave you?