When you create characters for a novel, it may help you to think like an animator creating characters for a cartoon: you want them to be distinct from each other not only in behavior, but also in appearance.
In a movie with real actors, distinctness comes from the distinct faces that humans have. In a cartoon, where the faces of the characters don't have the detail of real humans, the simplified features are exaggerated: one character has a very long face, another a very round one; one character has a long nose, another a protruding chin; and so on. As we don't always see a character's face, and want the character to be recognizable easily even from afar or in fast paced action, we also give them different colors and a distinct silhouette:
Example by Mike Corriero from The use of Silhouettes in Concept Design
In a novel, the reader cannot see the character. And even if you describe the outward appearance of your characert, you don't repeat that description every time that character is mentioned.
In a novel, the "face" of a character is his name.
Your readers can only tell John and Bob apart by their names. So make their names distinct enough.
But what is disctinct enough? Certainly Henry and John are distinct enough and no one will confuse those two characters. John and Joan will probably be distinct because those names strongly suggest different genders, although readers may interpret the similarity in their names as signifying some kind of relation between these characters. Such a relation will be expected when your character names are variations of each other, as in Henriette and Henrietta. The similarity between these names must be motivated or it will be irritating.
Similarity can lie in all parts of a name: the first letter (Henry & Horton), the vowels (John & Rob), the "rhyme" (Francine & Janine), and so on. Similarity is also relative: When you have only two characters in your short story, Ben and Rob will appear distinct enough, but in a novel with Hector, Fyodor, Maximilian, Wulfram, and Mordecai, the shortness, commonality, and similar sounds ("b") will make Ben and Rob appear quite related.
Personally, I try to make the names of my protagonists and main side characters as distinct from each other as possible. I even try to make them distinct from place names in the same novel – I don't send Allen to Alaska, for example.
At the same time, you shouldn't worry too much about similarities when they become too hard to avoid. If you have more characters than letters in the alphabet, they cannot all begin with their own letter. If you write a historical novel, you must use the names that people had, even if they had the same names. And so on. So I try for distinctness, but if other things become more important, some similarity doesn't give me gray hair, either.
What I find more important than distinctness, which usually is not difficult to achieve, is a name's meaning. And with meaning I don't mean the etymology of a name. Most readers will not know the etymologic meaning of most names, and if you make up names for a fantasy novel, that name will be etymologically meaningless.
But names suggest personal traits to us. For example, certain names – and names with certain elements such as a specific ending – are predominantly given to people of a certain gender and therefore suggest a certain gender when we read it. Most people in the US will think that John is a man and Sarah is a woman. In some cultures, names that end in "-a" are mostly female.
Gender is one meaning that names convey, age is another. Different names are popular at different times, and therefore different names are more common among people of different ages. Old-fashioned names, that were popular fifty years ago, will make readers think of people of middle age; names from a hundred years ago will make people think of old people.
While gender and age of a name are easy to research, there are other meanings that are more difficult to grasp. Marketers have researched the meaning of the sounds that they use to make up brand names; psychologists have researched how certain personal names suggest attractiveness, intelligence, wealth, humor, and other personal traits. This research is, as yet, in its beginning stages and very limited. Only a small selection of names has been studied, and only a small variety of traits; studies on the meaning of sound yield contradictory results for all but a small number of phonemes. But some people, for example the writer Ursula Le Guin, have a natural talent to "hear" this meaning and find names that fit their characters like a glove.
I cannot recommend a fail-safe strategy to find character names with a fitting meaning, but the question you link to has a lot of information on this aspect of naming and I strongly suggest that you consider it carefully.
You may want to avoid giving your characters names that have been used in other novels, especially if those names are rare or made up. Frodo is taboo, as is Harry Potter.
Other names appear to represent the stereotypical heroine, and many authors use a variation of them. For example, the name Katherine and its many variations and close relatives are given to such a large number of YA protagonists and movie heroines that it has become empty and meaningless. Some recommend to avoid Kate, Kay, Kathleen, Caitlin, Cathy, Cat, and so on for that reason; I think it makes that name a wonderfully neutral placeholder that facilitates reader identification.
The following is a list of some studies on sound and meaning in (English) brand names. Some of these articles may be paywalled, but may be accessible from a university library through their subscription. This list is the result of a very quick search I did when brainstorming the names for my last book and probably nowhere near exhaustive. But it may give you an idea what to look for and where to start. Use Google Scholar's "Similar Articles" link (below each search result) and the terminology in these articles to find related articles.
- Klink, R. R. (2000). Creating brand names with meaning: The use of sound symbolism. Marketing Letters, 11(1), 5-20.
- Klink, R. R. (2003). Creating meaningful brands: The relationship between brand name and brand mark. Marketing Letters, 14(3), 143-157.
- Lowrey, T. M., & Shrum, L. J. (2007). Phonetic symbolism and brand name preference. Journal of Consumer Research, 34(3), 406-414.
- Lowrey, T. M., Shrum, L. J., & Dubitsky, T. M. (2003). The relation between brand-name linguistic characteristics and brand-name memory. Journal of Advertising, 32(3), 7-17.
- Wichmann, S., Holman, E. W., & Brown, C. H. (2010). Sound symbolism in basic vocabulary. Entropy, 12(4), 844-858.
- Yorkston, E., & De Mello, G. E. (2005). Linguistic gender marking and categorization. Journal of Consumer Research, 32(2), 224-234.
- Yorkston, E., & Menon, G. (2004). A sound idea: Phonetic effects of brand names on consumer judgments. Journal of Consumer Research, 31(1), 43-51.
The literature I have on the "name-valence" or subjective perception of personal names all used German samples, because that is my target audience, and may not be useful to you. Try searching for something like "attractiveness names" and "personality names" on Google Scholar and again use the "Similar Articles" links and the terminology and bibliography in the articles you find, to find more.