Really it all depends on how things went down honestly. We didn't get to see exactly what happened after the event so we can't say for certain there wasn't looting and rioting, even with heavy military presence. I'm just guessing that things got chaotic enough, even with the bomb detonations so close, that rioting was an issue that people felt was dangerous enough to warrant boarding up their homes.
Like I said before, I could understand boarding the windows because of riots, but why board your door? Where will you live if you can't get inside your house? Since we see the wooden boards are nailed on the outside of the house we know that who boarded it was also on the outside.
It's possible the type of bomb played a role in how bad the rioting got, since the bombs used in the city are clearly not of the same type as ones used in Lonesome Road or at Vault 87. Their craters are much weaker and has less rads. Bad game design, probably, but I'm guessing IRL there's warheads weaker than others.
Judging by the Megaton crater and radiation after we explode it, the white house being just a giant hole in the ground with a really deadly type of radiation, Vault 87 entrance (that you mentioned) was hit by one nuke and still the radiation will kill you almost instantly, most puddles on the ground will radiate you too. I would say that the radiation from the Nukes who hit Washington DC was quite deadly (this is also supported in game by showing that the Nukes used in the Fallout universe differ from ours because they don't seem to have such a powerful explosive power as real world ones [because wooden houses are still standing, some almost unscathed] but they are way more radioactive than the real world ones, because the radiation from it can still be felt in the environment after 200 years old and some places can still kill you in seconds if you walk into them). If you can die in minutes just by exploring ruins in DC after 200 years imagine how much radiation that city would have had after the bombs fell. I would say anyone walking in it would have died in seconds (like Vault 87 or the White House, 200 years after the bombs).
There's also the possibility that they were boarded up post-war. Settlers seeking shelter may have boarded up a building to keep an enemy inside or to keep resources secure while they leave to find more elsewhere, presumably dying in the process.
I don't think anyone could have boarded up around 5 windows and two doors (depending on the house) while an enemy was inside without the enemy coming out of the house, unless the enemy is bound in some way, but if it is bound already there is no point in going as far as boarding an entire house to keep the enemy there (it would be much easier to just keep the enemy bound or kill it right away).
Unless the enemy is some kind of critter that can't open doors, but then there is no point in boarding them since the critter can't open the door.
I really see no way why someone would board their house in Fallout 3 universe.
Boarding a large house like that will take hours and require a ladder or something else (if it has more than the ground floor).
Also I don't see the logic of someone thinking to themselves "I will look for more resources in the wastes, so I will now board up my house to keep my remaining resources safe until I return with more resources. It will only take an hour to do so and make a lot of noise by hammering these boards, attracting attention to me and my house, and it will take some time again once I return to un-board it again so I can go back inside while carrying more resources. Also I have to do this everytime I go out to scavenge."