That is true, however it still gives the missile a far better chance against most countermeasures. The ship defenses have to perform perfectly, particularly if more than one missile is incoming.
More importantly, compare that with the response time for ship defenses against the American Harpoon and/or the French Exocet - 120 to 150 seconds. 3 seconds versus 150 seconds is a substantive difference. In one case the defenses have to work perfectly the first time (and far out enough to ensure that shrapnel and fuel from a successfully destroyed missile do not effect a soft kill on the ship by taking out antennae etc on top of the ship), while in the other case 150 seconds is enough time to try several times (and in several ways).
3 seconds reaction time doesn't make a missile invincible, but then what does that say about the ASM Tomahawk, Harpoon and Exocet?
The 3 seconds must be the time from detection to a firing decision. The designers must be counting on delaying detection until the missile is much closer than existing missiles. So it’s fast and stealthy. Stealth is relative, and speed is relatively insignificant in the computer world. I think something traveling at better than Mach 2 would stand out like a sore thumb on pulse Doppler systems. That’s not even counting such things as skin temperature (hotter than surrounding at that velocity) and detection on the electromagnetic spectrum (active targeting system?).