Since I haven't figured out the nifty multiple quotes thing....
As to the WF: Handguns - He and Watson both shoot at the Andeman Islander in "Sign of Four" and at the hound in "Hound of the Baskervilles". As The Monster said, he decorated the wall with VR (mentioned in "The Musgrave Ritual"). It appears he knows how to use a pistol, he'd just rather not. (He does pistol whip a couple of guys, however.)
As to Irene Adler, define "a woman of character" There are a number of undertones in "Scandal" showing that Holmes respected Irene quite a bit, and not only as the winner in their match. The last line of "Scandal" is "He used to make merry over the cleverness of women, but I have not heard him do it of late. And when he speaks of Irene Adler, or when he refers to her photograph, it is always under the honourable title of the woman." IMHO, the disad should remain, or perhaps be modified slightly. Holmes does get in one good snark at the "King" after he remarks that Irene would have made a good queen if she were "on [his] level”.
“From what I have seen of the lady, she seems, indeed, to be on a very different level to your Majesty,” said Holmes coldly.
He also turns down an emerald ring in payment in favor of her photograph.
And as to Watson referring to her as "the late Irene Adler", in the Victorian period, that didn't necessarily mean she was dead, simply that she was no longer a point of interest.
(Can you tell I like Irene?)
As to the DNPC for Watson, I see him more as an ally or contact than a DNPC. He's very capable and (as discussed above) intelligent. He has useful combat skills as well as noncombat skills ("Quickly Watson, get your service revolver!"). SH refers to himself and Watson as "this agency" ("Sussex Vampire") and depends on Watson to protect their client and to investigate in "Hound of the Baskervilles". I just don't see him as a DNPC.
Holmes is, however, very protective of Watson. In "The Three Garridebs", he tells the forger "If you had killed Watson, you would not have got out of this room alive."
He needs a KS: Music. He wrote a monograph on the Polyphonic Motets of Lassus ("Bruce Partington Plans). He often attends the opera and concerts (in "Study in Scarlet", he wants to wrap up the investigation so he can go hear Norman Neruda play the violin).
He needs Cryptography - "I am fairly familiar with all forms of secret writing, and am myself the author of a trifling monograph upon the subject, in which I analyse one hundred and sixty separate ciphers." ("the Dancing Men").
He needs SS: Physiology - he recognised the relationship between the three sisters by the shape of their ears ("Cardboard Box") and later identified one of the victims by the shape of her ear (which was all he had).
He also needs Tracking (“Study in Scarlet”, "Silver Blaze", "The Priory School", "Hound of the Baskervilles", "Boscombe Valley Mystery"), SS: Ballistics ("Reigate Squire" and "The Empty House"), SS: Psychology ("Scandal in Bohemia", where he lures Irene Adler into betraying where she had hidden a photograph based on the "precis" that an unmarried woman will seek her most valuable possession in case of fire, whereas a married woman will grab her baby instead.) and probably a dozen other things I've forgotten.
Mary Ann