Let's say that I'm playing on my computer and, according to the game's design, end up getting 50FPS for the 3D stuff and 20FPS for the 2D stuff. The theory would be that everyone gets 20FPS for the 2D stuff because we're going to mess with it for gameplay purposes.
Along comes the guy who drops that EMP. Everyone within range gets dropped to 5FPS HUDs. It doesn't matter if they're getting 200FPS or 60FPS for the rendering of the 3D environment because the frame rate of the HUD has become a gameplay issue. So it must naturally be throttled and uniform for everyone.
Yes, the 3D rate could rise when the 2D rendering is slowed, but it doesn't have to. I'd argue that it shouldn't, so that the player gets a more uniform experience out of the game. I find stuff like that distracting.
So anyway, I'm jumping in here to observe that the HUD display rate would become a gameplay issue if @frag971's suggestion was implemented.
I don't love the idea of being the guy in the ship that got disabled. Being in a disabled ship is not why I got into the game. An EMP should impair, but not disable a ship. The Planetside 2 guys understood that. Their weapon exists to temporarily disable systems on the player's character, not completely prevent it from operating.
Don't blind the pilot. Don't take away his ability to maneuver. Those are severe breaks in gameplay. Temporarily remove one aspect of his capabilities and leave it at that. Per Planetside, drop a ship's shields and short range sensors. That seems perfectly matched to what an EMP does. I'd leave the HUD up, but without any short range information on it. Or just some random information. Force the players to temporarily rely on their Mk I Eyeball to maintain situational awareness.