I think it is unlikely both Brandon and Willoughby missed their shot because neither seem to be a slouch with a gun—in Chapter 9 Sir John says Willoughby is “A very decent shot” and Brandon was in the army and seems to be enough of a sportsman to be held in high esteem by Sir John so although I cannot find specific proof in the text I feel keenly the colonel’s shooting skills are probably fine. I agree with you that it is more likely that they both deliberately missed than accidentally missed. * Duels were fought to settle questions of honor and I think if the Challenged does something which admits to the dishonor of what he is done then the point is made without bloodshed and that is what could have happened between Brandon and Willoughby. It may have been Willoughby shot into the air or threw his sword down (or some such dramatic act) and the admission of his wrong in front of the witnesses I am assuming are in attendance is enough for Brandon who IMO even in this situation would not be blood thirsty.

On one hand I think the idea that Willoughby admits to the truth in this secret meeting is still hard to swallow because he cannot even admit to Marianne the truth of his dealings with her when he is found by her at the party in Chapter 28 or in his letter to her in Chapter 29 but on the other hand Willoughby is a coward not admitting the truth to her and perhaps he is also being branded a coward for not defending himself when challenged. Perhaps Willoughby was unwilling to take a wound for his actions and gave in for that reason—but for whatever reason there was not bloodshed and regardless I think Brandon would not have left without some satisfaction either by wounding him physically or by his admission of guilt before others. IMO Willoughby admitted he was guilty of what Brandon accused him, something which might have hurt his ego almost as much as a gun shot wound. (;D)

* This is the explanation in The Norton Critical Edition of S&S on this passage in the text: Met to duel. Through illegal and widely criticized throughout the eighteenth century dueling remained the customary means by which gentlemen settled questions of honor.