3 seconds is a very, very long time for modern computers.
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?
That three seconds includes slewing and firing a CIWS or RIM-116 point defense weapon to the firing solution, engaging the target, and destroying it.
Also, at Mach 3, even if you hit the missile the supersonic shrapnel will make for a bad day onboard the targeted ship.