We have real hardwood flooring, and it seems to be impervious to liquids. I would guess that this might vary, however, with the fit of the individual pieces and the type of finish. The pre-finished stuff might be worse in this regard, since there is no continuous polyurethane barrier to prevent liquid from getting into the gaps.
You might want to contact your vet, or have him/her refer you to a bahavior modification specialist. Some people think that this is hoakey, but in reality it works very often and is, in the long run, sometimes much cheaper than working around the problem.