I would like to know if "hob" can be considered as a prefix, and if yes, does it have some meaning, at least vague? I am thinking in particular about words hobgoblin, hobnail, hobnob...
In general, "hob" shouldn't be considered one prefix. In the first two cases you list, "hob" is actually two different prefixes. The "hob" in "hobgoblin" is a colloquial synonym for "Robert". The "hob" in "hobnail" comes from the term for a blunt projection of some sort
In the third case, I don't believe "hob" is a prefix at all, since "hobnob" is a combination of two verbs. Here, "hob" comes from the verb "to have."
Source: comparison of etymological dictionary entries for each word (in particular etymonline.com)