I've never been sure whether it means "effective against 99.9% of species of nasties" or "will kill 99.9% of the organisms in a given sample". The latter leaves a lot of questions vis what organism, concentration, time period, etc.
I believe there are standards for categorising disinfectants by relative efficacy against standard organisms compared to simple chemicals (acids, oxidisers and the like). Sort of thing that the stuff used in labs and hospitals will have gone through, but probably not your lemon-scented Frish (other than perhaps as an advertising standards thing).
Killing bacteria by b0rking the cell membrane isn't rocket SCIENCE, and pretty much anything soapy will do it. Spores and things can be sturdier.