Yes, as Thrakhath explains in Wing Commander II, the Ghorah Khar rebellion sets back development and production of cloaked fighters by eleven years. Production of Strakha doesn't resume until 2667, and then only in very limited numbers. We're told several times that the first small amounts of them are usually reserved for reconnaissance missions. Strakha seem to be a bit more common in the last weeks of the war, but the element of surprise is gone by then.
The reason the Tiger's Claw was destroyed so easily was because no one suspected that a completely invisible ship could exist... not because they're absolutely invulnerable. As you should all know from playing the games, intercepting a stealth fighter isn't impossible -- it just requires that you alter your tactics to adjust to them. Think of American Wildcat pilots coming up with special maneuvers to counter superior Japanese Zeros early in the Pacific War.
Anti-cloaking weapons were also developed very quickly. The Confederation had premiered the "Anti-Cloaking Gun" before the end of the war (in the Armada addon, Proving Grounds). In Wing Commander IV, we see the technology integrated into the new Lance fighters -- you can always see a white 'outline' of any cloaked fighter when you're flying one.
(And, of course, humans developed their own cloaking devices immediately, too. Shroud Devices were being used in combat in 2669, and a fully cloak version had been succesfully tested before the surrender. Once everyone has the bomb, no one has an advantage.)
