BEagle
The 787 main deck floor is an integral part of the fuselage barrel - it's not all bolted together like it is on aluminum aircraft. So strengthening the floor for cargo is non-trivial. A production freighter would require a complete redesign of the fuselage barrel (and likely new tooling), while retrofit would be a nightmare.
The 787's floor is not integral to the fuselage barrel. See link below.
Boeing Images - Search Result
The fuselage barrel sections are indeed baked as in integral unit, but those sections do not include the floor beams or even the floor beam attach fittings. Indeed, not even the frames (ribs) are integral to the barrel sections, only the skins and longerons (excuse me, my Douglas is showing. Boeing calls them stringers) are integral. The frames are bolted on later (as opposed to riveted for aluminum airplanes) and then the floor structure is bolted to the frames. ZA005, the only 787 flight test aircraft that has been refurbished and delivered was refurbed here in San Antonio. We did a LOT of work on the main deck floor beams, floor boards, and seat tracks. And yes, those floor boards and floor beams all come out and can be replaced.
Personally, I doubt that an airliner will ever have an integral floor. Why? Heavy maintenance and mod. Heavy maintenance and mod is what we specialize in here in San Antonia and doing that on an airplane with an integral floor would be a nightmare. There's a LOT of stuff that runs under the floors that would be really hard to gain access to if the floor was integral to the fuselage. Especially over the wing where there is no lower lobe.
I think the bigger issue will be adding a freighter door. That 787 fuselage barrel is glued together and baked in an autoclave. You can (relatively) easily add doublers and other parts to beef up an aluminum structure to compensate for a big hole cut in the side. I have no idea if that is possible for a plastic fuselage. At least today. If history holds, Boeing and Airbus will have about 20 years to figure out how to do that.