You are spot on.
So what happens to the electronics connected to a radiotelescope when it gets struck by lightning? Does research stop while equipment gets replaced every time?
A lightning strike does not couple across every single non-shielded circuit path. You can protect from a lightning strike using a surge protector since it has a point of origin. EMP affects the entire facility at the same time. Think of it as a field coupling to every single wire (even exposed circuit runs in a circuit board).
In the end, the real issue with EMP is the power grid. The power grid will largely go off-line, and certainly will break grid tie-points.
We need to figure out how to bring power grids up hot from a cold state more quickly. It is an incredibly complex problem, but one that can be solved, (and practiced).
That may be a good way to get new power transmission paths past environmentalists - use the "EMP" hardening argument.
Power companies, transmission companies would do well to preposition all the spares needed to make grid recovery a faster process.
On the other hand, if the EMP hysteria is correct, Best Buy is a good stock to invest in......all that consumer electronics will need to be replaced!
Exactly!