I was only commenting on how impactful it would be if we had after 9-11 (or in the future) wound up with actual restricted areas around all these places instead of an advisory.
First, it's not an advisory, it's a regulation. But it does allow you to overfly as long as you don't linger, and that was your concern.
Second, as for creating Restricted Areas over those sites, they don't meet the legal requirements for creating a Restricted Area, specifically, activities which are hazardous to nonparticipants. In order to create a permanent ban on overflight on the basis of national security, they'd have to create Prohibited Areas like the ones over the King's Bay and Bremerton sub bases, and I don't think they'd be able to make the legal case to do that.
... it would be difficult or impossible to transit the Gorge without going within a mile or less of Bonneville dam.
Perhaps Randall misread the NOTAM. It does not prohibit overflight, just "circl[ing] so as to loiter" over those facilities. So he can certainly transit that area passing within a mile of the dam without violating that rule.
Here in Oregon something like that would seriously hamstring VFR pilots wanting to get from west to east of the Cascade mountain range when weather is below 5000' or so... the Columbia River Gorge is how we do that, and the ceiling doesn't have to be low at all before it would be difficult or impossible to transit the Gorge without going within a mile or less of Bonneville dam. And of course our little GA aircraft are no threat to dams. If you watch any WWII documentaries (and who doesn't?) you know that it would take a BIG aircraft with a whole lot of explosives to do much damage to one.