I think that's it, it's a subtle way of teaching kids respect for their elders. In the beginning, characters like Gordon, Susan, Bob, and especially Maria and David were a lot younger (and they were also progressive characters) and were regarded more like everyday friends for the kids - both on the street, and watching at home - so it probably wasn't much of a thought process to have these characters refered to by their first names.
Mr. Hooper, on the other hand, was a respected elder in the community. Similarly, Mr. Handford was also a respected elder - a retired fireman who had bought Hooper's Store because he was tired of being retired and wanted something to do. They were treated almost more like parental figures, as opposed to their younger predesessor, Alan, who, like the aforementioned other humans, was seen more like a friend to the neighborhood kids rather than a parental figure.
But again, the thing to remember too is that SS was a progressive, and somewhat subversive show, even from the beginning . . . some adults with that mindset actually prefer that children refer to them by their first names instead of Mr. or Mrs. So-and-so, despite it traditionally being the proper thing for children to do. It's sort of similar to TO KILL A MOCKINGBIRD, how Scout refers to her own father by his first name, because she believed that children and adults should treat each other as equals.