That's an interesting connection, however, I don't know that it was an intentional reference. Likely, Lynch might agree it was part of his subconscious while creating the show, but apparently it was Lynch's tribute to the restaurant chain, Bob's Big Boy:
Frank Silva, who plays BOB, says the name is Lynch's tribute to Bob's Big Boy, the place where he had the same lunch every day for years.
From Lynch's book "David Lynch: Interviews":
I like things to be orderly. For seven years I ate at Bob's Big Boy. I would go at 2:30, after the lunch rush. I ate a chocolate shake and four, five, six, seven cups of coffee--with lots of sugar. And there's lots of sugar in that chocolate shake. It's a thick shake. In a silver goblet. I would get a rush from all this sugar, and I would get so many ideas! I would write them on these napkins. It was like I had a desk with paper. All I had to do was remember to bring my pen, but a waitress would give me one if I remembered to return it at the end of my stay. I got a lot of ideas at Bob's.
This may be speculation, or merely what Frank Silva (who plays BOB) was told by Lynch, however, considering his origin myth, it makes some sense as a play on what Leland has become now that he is a "big boy" and basically owned by BOB:
When Leland Palmer was a boy, BOB lived near his grandfather. He taunted Leland, asking "do you wanna play with fire, little boy?" BOB subsequently possessed Leland.
(From: http://twinpeaks.wikia.com/wiki/BOB)
Apparently, BOB was not originally part of the show as Lynch conceived it, per, "The Terror Of “Twin Peaks”: His Name Is BOB" by Matthew J.X. Malady:
“In the beginning,” as Lynch noted during a talk he gave in Seattle a number of years back, “there wasn’t any BOB.” While shooting the pilot in an Everett, Wash., home that would be used for the Palmer residence on the show, a member of the crew joked to Silva, the set dresser, that he needed to make sure he didn’t trap himself in Laura Palmer’s room in the process of setting up for a scene. When Lynch heard the comment, it triggered something. “In my mind,” Lynch continued, “I see Frank locked in that room. And I went rushing in to Frank, not knowing why I rushed in, really.” He asked Silva if he was an actor, to which Silva answered in the affirmative. “So I said, ‘Frank, I think you’re going to be in this scene.’”
Lynch then filmed the takes, first broadcast during season one, where Silva, as BOB, crouches down at the edge of Laura Palmer’s bed, “but I didn’t know what in the world, you know, Frank was doing there.” Later that night, Silva (who passed away in 1995) seemingly ruined a perfect take featuring Laura Palmer’s mother by accidentally standing in a spot where his image was reflected onto a mirror behind the actress playing Mrs. Palmer. The occurrence seemed to cement things for Lynch, who saw it as something that was meant to be and included the botched take in the final cut.
...but you are correct that his "proper" name is "Robert":
The first insinuation of BOB occurs in the series pilot, when Agent Cooper digs deep below the recently murdered Laura Palmer’s left ring fingernail with tweezers and — as we see in close-up detail — removes a tiny piece of paper with the letter “R” typed onto its surface. Later in the series, viewers find out the killer was spelling out ROBERT by leaving these letters on his victims’ bodies.
Other than that, I don't think there's any other character names which have any special meaning.
