Fun question!
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.cometymonline.com)
