I've seen lots of people claim that about (especially downtown) SF; the normal claim about the rest of the Bay Area is that it's unaffordable because of the people that want to keep it habitable, not that it is uninhabitable.
> I assume "Muni" means buses or cable cars
The San Francisco Municipal Railway operates busses and cable cars, sure, but also surface and subway trains which share several of BARTs dowtown underground stops, but also have a lot more stops in the city that are not shared with BART.
> and I will only say that during wandering around for ~20 hours, I didn't see a single bus, so I conclude Muni doesn't service suburbs.
It doesn't (that I know of, there may be some lines that go out of the city, certainly many non-SF operated lines go into the city); there are many other transit agencies in the Bay Area, many of which have bus lines in the suburbs, including lines that run into the city. The area right around SFO (excluding the airport itself) may be a relative dead zone, I haven't really spent much time there.
I wouldn't generalize about the Bay area from a few days in a particular corner of San Mateo County, though.