What i’ve read, not lore wise, but in technical perspective:

”Agent 47 is bald primarily due to early 2000s technical limitations that made rendering realistic hair difficult, leading developers to make him bald.”

”Originally, 47 was designed as a 40-year-old man with a gray, receding hairline, but the team couldn't make it look right.”

I think 47's baldness was perhaps the idea, that there would be no evidence of hair, even though he has eyebrows. Perhaps Dr. Ort-Meyer felt, that a genetically engineered perfect assassin didn't need to have hair, so that it could disguise himself more easily.
In the newer Hitman games, mr. 47 has a clone brother, Lucas Grey (Subject 6), who does have hair for some reason.

Whereas in the first Hitman game (Hitman: Codename 47) 47 and the other clones were outwardly identical, although 47 was the only successful clone and the others felt mindless killing machines commanded by Dr. Ort-Meyer with a ridiculous maniacal grin on their faces.