Can a metal pipe shield wiring against EMP during a nearby lightning strike?
Strictly speaking, in regards to your original post, yes - grounded metallic piping will act as a Faraday cage and can shield wiring and electronics from EMP. To be useful, the whole system must be encased, which may be practical or not. Likely, a conduit could be run directly from the generator to the control panel/annunciator.

Watch out for other signal paths, though. Generators having wiring harnesses that would be impractical to encase, and may need shielded wiring.

As an aside, EMP damage has been assumed here, and may not actually be the case. I still urge that you have the board closely analyzed. Having to replace the board anyway, you might be able to get one with better isolation that isn't susceptible to the kind of failure the original board suffered.