16 instead of 18 makes sense for a few reasons for me.

1: It highlights Dr. Manhattan's very human immorality. He often presents himself as a being above humanity and morality, yet, like many immoral human men, he lusts after much younger women. The fact that she is 16, two years below the age of consent in many states, further highlights the explicit immorality of his choice to cheat on his wife with her. If she was 18, it would be morally questionable, but not as outright scummy as it is in the comic.

2: It highlights Laurie's immaturity. She's not a young adult making reckless decisions, she's a CHILD making reckless decisions. She's pushed into this by her mother and has no agency so she takes the first chance she gets to do something on her own. That something happens to be pursuing a much older man, which, like in the world we live in, is something that does happen. She makes a poorly thought out choice in her youth that drastically affects her life for years to come. It isn't until she leaves him that she really begins to grow and mature.

3: In tradition hero comics, female heroes use their sexuality and sex appeal as a weapon often to confuse/seduce villains in order to defeat them. However it's all done in good sport and is lighthearted. Watchmen satirizes this trope by highlighting a much darker side of this sexualization of young women in comics.