My problem with Before Dishonor and the humor is that, while I agree with you about the small element of humor/irony (to a point), this book was too much like a New Frontier novel, with quite a bit more than a small element.
And I can only speak for myself, but I didn't really want humor in this story. Irony works, but not humor. We're talking about a giant Borg Supercube that has the possibility of succeeding where other Borg vessels have failed. If I had been working in the Operations Center (or wherever Jellico and Nechayev were) and hearing the two senior-most Starfleet officers talking like that, I'd have gone "What the f***?!" I thought it was a bit inappropriate, and reinforced my not take anything seriously about what he was writing. Part of why Destiny worked for me is because I could take it seriously. While I didn't think it would be endgame for the Federation, part of me was always thinking "Crap, this could be the end of the road..." all the time.
With Before Dishonor, I kept thinking "What the hell? Why did that happen? Jeez..." In the review thread I had posted a while back, I mentioned how, every time I read any book, but especially Trek Lit, I have snacks of some sort. The less I enjoy the book, the more snacks I need to get in order to power through the book. Before Dishonor set the record for the most snacks needed to get through. It got to the point where as soon as I was done, both reading and eating, I went and vomited (not because of the book, but because of the food).