Yes they did. One of the other members of the crew turned to Worf and asked him why the Klingons in the past looked so different, he just grumbled "We don't like to talk about it" and that was it. I'm not aware of what the real story is.

They appreard human like because of genitc experimention its a bit long winded but it explains everything. Augments were born in the late 1960s as the result of an ambitious project to improve the Human race. Scientists used a selective breeding program combined with genetic engineering to achieve their aims, and in many ways, they succeeded; the "supermen" were mentally and physically superior to ordinary men and women. They were roughly five times stronger than the average person, their lung efficiency was 50 percent greater than normal, and they had an increased capacity for learning. What the scientists failed to anticipate was that creating a superior race meant creating a superior ambition; the "supermen" felt that their advanced abilities obliged them to benevolently rule the rest of "primitive" humanity. [edit] The Eugenics Wars In 1992, a group of "supermen" seized power simultaneously in more than 40 nations. Khan Noonien Singh was considered the most dangerous of the ambitious cadre. At his most powerful, Khan ruled all of Southeast Asia and half of the Middle East — more than a quarter of the entire planet — but even this was not enough for him. He envisioned ruling the entire world, but so did the other genetically engineered leaders, and they ended up fighting among themselves, leading to the Eugenics Wars, during which whole populations were bombed out of existence and Earth was threatened with a new Dark Age. Fortunately, by 1996, the tyrants were brought under control by a rebellious population. Most of the "supermen" died or were sentenced to death, but 84 of them, including Khan, escaped aboard the sleeper ship SS Botany Bay. This vessel would later be encountered by the starship USS Enterprise more than two centuries later. Although initially civil (if forceful) toward Captain James T. Kirk and his crew, Khan's desire for power and conquest made him too powerful to be allowed to roam free. After a failed attempt at taking over the Enterprise, Khan was exiled to Ceti Alpha V, an uninhabited but habitable planet where he would be allowed to reign. Several months later, a nearby planet, Ceti Alpha VI, fragmented and broke apart, destroying Ceti Alpha V's environment. Over the next 16 years, Khan and his followers suffered on the planet, abandoned by Starfleet. Eventually, they were able to hijack the starship USS Reliant and attempt to take their revenge upon Kirk. [edit] Arik Soong and Augments Unknown to Khan, some eighteen hundred discarded Augment embryos from the 1990s were left behind on Earth and preserved. After the founding of Starfleet, the embryos were stored at the Starfleet Medical facility Cold Station 12. Dr. Arik Soong, director of the facility, stole 19 of the embryos. Like Khan, he felt that it was a tragic waste that the senseless destruction wrought by the Eugenics Wars had been allowed to taint policy and views regarding genetic engineering for centuries afterwards, and believed that if he could prove with his Augments that the Wars had been isolated and improbable events, that he could convince the government to rethink its stance on the issue. Soong secretly brought the Augments to a remote, secluded planet, and raised and schooled them as his own children. The Augments were indoctrinated at an early age to the idea that they were far superior to Humans both physically and mentally. When Soong was incarcerated, the Augments were left to fend for themselves for a number of years, a fact which hardened them and made them resentful of the inferiors who took their "father" away. Eventually, they escaped their planet and commandeered a Klingon Bird-of-Prey, killing the crew with their bare hands. They subsequently took hostages at CS-12 and were reunited with Soong, who sought to obtain thousands more Augment embryos. (Interestingly, the Augments themselves did not know of Khan's sleeper vessel Botany Bay, which Soong dismissed as a "myth," as all records concerning its launch were destroyed.) Ultimately, the Augments were destroyed by Enterprise (NX-01) when they refused to surrender their nearly-destroyed Klingon Bird-of-Prey, although Soong himself was recaptured. [edit] Augments and Klingon experiment The ability of the Augments to defeat a group of Klingons caught the interest of the Klingon Empire, which was able to obtain a few surviving Augment embryos which were used in genetic experiments to augment Klingon DNA. However, the experiment went wrong when the Human Augment DNA proved to be more dominant than the Klingon genes, and mutated into a deadly virus that quickly transformed many Klingons into Human-looking creatures. A cure was found to keep the virus from being lethal, but did not change its appearance-altering effect. Since the vast majority of Klingons were afflicted, they were left with the more Human-like facial appearance for a few centuries. (This story was written to explain the apparent discontinuity between the Human-like Klingons seen in the original series and the more obviously "alien" Klingons from the Star Trek movies and later television series. In the Star Trek: Vanguard novel Summon the Thunder, these Human-appearing Klingons are referred to as QuchHa', or "the unhappy ones.") [edit] Late Federation augment experiments Star Trek: Deep Space Nine revealed late in its run that Dr. Julian Bashir was the subject of similar augmentation experiments that gave him acute mental and physical abilities.

I think it was more of a creative decision, without substantial backstory to explain it. Worf's comment (cited in response 2) is poking fun at this fact.

Much like religion, you ain't supposed to question tv & movie plots because it ruins the ending