Yes, it does make a slight but significant difference. The reflexive has two distinct uses, helpfully covered in the Oxford English Grammar (OEG) 4.40 and 4.41.
The first is what OEG calls primary reflexive pronouns, which contrast with emphatic reflexive pronouns.
- Primary reflexive pronouns are defined in OEG as follows:-
The primary reflexive is used in place of a personal pronoun to signal that it co-refers with another nominal in the same sentence or clause; that is to say, they both refer to the same entity....
In case that is not clear, here are two examples (not form OEG)
a. When he realised the Battle of Philippi was lost, Brutus killed himself.
Here, the proper noun "Brutus" and the reflexive pronoun "himself" refer to the same 'entity' (here a person).
b. She always washes herself thoroughly after feeding the pigs.
Here, the pronoun "she" and the reflexive pronoun "herself" both refer to the same 'entity' (here again a person). The subject and object of the verb are one and the same.
- Emphatic reflexive pronouns are defined in OEG as follows:-
The emphatic reflexive is used in addition to another nominal to emphasise that nominal.
So in your sentence:
c. Though dead for three years, the ghost of this scoundrel threatened greater harm to Sherlock Holmes than Professor Moriarty himself had done.
The "ghost" in this sentence is, of course, the ghost of Moriarty, the evil genius of Conan Doyle's stories. Its use here does not change the meaning of the sentence, in the sense that it does not change the conditions for its being true or false. Here it emphasises the difference between the 'ghost' (ie a memory rather than the living person) of Moriarty and Moriarty's previous living reality. Other examples from OEG are:-
d. They also provided videotapes, which they selected themselves, of the high points of her interrogation.
e. In 1989, as often as not, the principal fights in the major campaigns are prompted by the ads themselves.
f. Mr McGovern himself had said repeatedly that he intended to stay on untilhe reached conventional retirement age.
Greenbaum of OEG goes on to explain this usage in more detail
Emphatic reflexives function as a kind of appositive (cf 5.11) to a noun phrase, which they emphasise. If that noun phrase is the subject, the reflexive may either immediately follow the subject or occur at various positions later in the clause.
So does it matter (make any difference to the meaning) if we leave an emphatic reflexive out? Well, as I have said, omitting it does not exactly give you less information in the sense that with or without the reflexive, the facts and so the truth value remain the same. But something is lost, and that is what might correctly be called an implicature: that is, something not directly stated but in a subtler way communicated to the hearer/reader.
Imagine I am trying to make a complaint about a suit I have bought in Ted Baker. I am speaking to an assistant and I say:
g. I do not want to speak to you, thank you. I want to speak to the manager herself.
I am communicating more than my wish to speak to a different person. I am 'giving you to understand' that I do not think you are senior enough or competent to deal with my complaint, and want to take it right to the top 'from the monkey to the organ grinder'.
h. Don't worry, madam, I shall deal with it myself.
The implicature here is: "You are a really important customer and you deserve nothing less that the best (i.e. me myself). In neither g nor h have I actually used or even thought the words added here. But there is a hint of the kind.
In the Sherlock Holmes example, the emphasis is literary and conveys a paradox. You would expect that with the devilishly cunning Moriarty dead, Holmes would have nothing to worry about. But in this sentence, it turns out that the very opposite seems to be true! And by the way, the word 'very' here is being used in a very similar way to the emphatic reflexive. It takes quite a few words to explain what these little words do, which is what makes them so potent.