I don't believe that any one particular person vandalizes the house, per se. The scenes with the future home all gutted and ratted out are very reminiscent, to me, of what happens to unattended vacant homes.
I've seen many homes look like this after sitting for an extended period of time empty, especially after they've been fenced off. That type damage is always from squatters that turn the home into a drug den. It's almost like the fencing-off creates a situation where the druggies feel safer, and the neighborhood residents typically let it slide (for the most part) figuring that the cops will deal with it at some point, but they rarely do.
What it conjures up in my mind is that, at this point, the Whites are done living there. It will remain vacant and unlived in for the remainder of the show. I foresee the DEA (or APD) seizing it in an upcoming episode to conduct an investigation into the Whites, and then leave the home empty.
The implication of the condition of the house, when Walt's future self goes there, is that it's been empty long enough to have been gutted out by drug users looking for some shelter to shoot up in, hang out, and so forth.
Symbolically, IMHO, it demonstrates the final failure of Walt to keep the tangible, first-person, evils of the drug world from destroying his home, and ultimately, his family.