I don't want to claim to be an EW expert, but I think you still have enough warning to turn the jammers on, pop chaff, etc. I agree that the time factor will make them more effective in this regard, but I don't think it has a huge impact.
One thing to consider is the flight profile of most supersonic missiles. They're gas hogs, so if they're going to have any range, they have to fly at high altitude. Older missiles like the Kitchen are high divers; they stay up high until they're terminal. AEGIS or other modern SAM systems can deal with those rather easily today. More modern supersonic missiles (including the Brahmos) use a high-low profile, where the missile cruises at high altitude until the radar finds the target. It then dives for the surface, gets below the radar horizon and closes the distance to the target until contact is reestablished and it goes terminal. This profile allows for counterdetection by radar and ESM when the missile first searches for the target, which means they know they have to switch their jammers on, orient their ship to the missile to maximize ECM effectiveness, and start puking chaff. Also, by being larger and faster, they are easier to detect on radar.
FWIW, I can't wait for the RATTLRS, but right now subsonic seaskimmers have a proven track record of success, while their larger supersonic cousins have yet to be used in combat (at least in an antiship role).
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