Except Bakula did have likeness approval for the QL novels -- I know because I heard a great deal from the editors at Ace on the subject while those books were a going concern. I guess he didn't have the rights for comic books, but he most definitely had approval over novel covers.
(The reason why later QL novels all had Sam wearing a hat was because Ace got tired of asking Bob Larkin to redo the paintings over and over again because Bakula kept complaining about the hairline.)
Normally I wouldn't quibble with KRAD, one of the more knowledgeable geek-pros in the field. However, in this case, he's COMPLETELY wrong...
I couldn't recall Sam with a hat from any of the books (I've since sold), and I wasn't sure how the timeline of comic publishing vs. book publishing was. So, I did a little Googling, and voila
This page shows ALL the novel covers:
Notice anything about Sam in a hat? Nope. Because he doesn't wear one. Ever
Heck, even Dean Stockwell's only in a hat on TWO covers ( a UK-only one from 1990, and a US one from 1997)!
So, while Stockwell (not Bakula) *MAY* have had problems with Larkin's coverage of him, it apparently wasn't terribly widespread, happening only twice in seven years!
As for the comics, they predated the US books. The comic ran September 1991 to August 1993. The UK novels began in 1990 and the US novels began in November 1992.
Here's the comprehensive comic page link:
Note that Sam IS
wearing a hat on three of thirteen covers here (NOT mandated by Bakula, but by the story) as he's a bus driver, a Santa, and a reporter doing a Clark Kent pastiche.