It's from the Lil Abner comic strips. It was the name of the place where they brewed moonshine from dead skunks. The name was adopted by Lockheed for their operating team perhaps as a result of the look and smell of their "factory" during the shooting star project, 1943. Hope this helps.

Term origin The Skunk Works logo as seen on one of Lockheed Martin's hangars.The term "Skunk works" came from the then-popular Al Capp comic strip Li'l Abner, which was popular in the 1940s. In the comic, the "Skonk Works" was a backwoods still operated by Big Barnsmell, known as the "inside man at the Skonk Works." In his secret facility, he made "kickapoo joy juice" by grinding dead skunks and worn shoes into a smoldering vat. The original Lockheed facility, during the development of the P-80, was located downwind of a malodorous plastics factory. According to Ben Rich's memoir, an engineer showed up to work one day wearing a Civil Defense gas mask as a gag. To comment on the smell and the secrecy the project entailed, another engineer, Irving Culver, referred to the facility as "Skonk Works". One day, when the Department of the Navy was trying to reach the Lockheed management for the P-80 project, the call was accidentally transferred to Culver's desk. Culver answered the phone in his trademark fashion of the time, by picking up the phone and stating "Skonk Works, inside man Culver". "What?" replied the voice at the other end. "Skonk Works" Culver repeated. The name stuck. Culver later said at an interview conducted in 1993 that "when Kelly [Johnson] heard about the incident, he promptly fired me. It didn't really matter, since he was firing me about twice a day anyways." [1] At the request of the comic strip copyright holders, Lockheed changed the name of the advanced development company to "Skunk Works" in the 1960s. The name "Skunk Works" and the skunk design are now registered trademarks of the Lockheed Martin Corporation.[2] Hope I Helped!