When I pulled the old plywood out of the Overlander, I noticed some areas of rot but nothing that smelled particularly bad. Bleach (sodium hypochlorite) is essentially a disinfectant. I'm not sure how much you really gain by bleaching the plywood in the long run... unless you plan to use the floor as an operating table.
I'm guessing any smells in the coach are more related to things other than the subfloor.
As for Pergo, I've installed in a residential application, but we decided against a floating floor in the Overlander. Pergo (and the ilk) offer a range of underlayments. If you're going with a floating floor, I don't think underlayment would hurt anything... except to shave a bit of headroom.