I would answer a firm "yes" to the question of physical differences between genders. I think that there is a difference in the physiques of male and female in just about every breed - with the males being somewhat heavier, or more 'substantial' than the females (hey, it's true in people too

). In the boxer, there is a difference in the amount of 'bone' - which is quite visible in the head, and general substance of the dog. There are also necesary structural differences - primarily around the shape and length of pelvis that also affect the overall look of the dog. Males are often more muscular as well, and have less 'shape' to the body (or are squarer, depending on how you choose to look at it).
I guess you could sumarise that by saying that within any chosen breed, dogs tend more toward substance and bitches toward elegance. Each judge probably has a slight preference for one over the other, though even that may vary between breeds.
As for which gender does better in the show ring - well, again I think that males do better overall. Of course, the two genders do show in separate classes until you reach the Best-of-breed (etc) stage, so below that point it is irrelevant. But my experience is that the BOB award (and thus the opportunity to compete for Best-of-group and Best-in-show) more frequently goes to males than to females. Same for most of the other "best-of" awards, other than puppies.
There could be a number of valid explanations or contributing factors for that though, it's not necessarily bias

Dogs are generally in their prime at around the 2-5 year range, and thus most likely to be doing the bulk of their winning at that age. It is relatively rare for puppies and young dogs to win a BOB award - partly because they are immature, but also because judges have a slight (natural) aversion to giving that award to a dog that is not yet "the final product". Now, bitches are in their prime during those years too - but they're also most likely to be bred from during that time. So there are more likely to be breaks in a bitches show career, and of course, her 'figure' affected by whelping and raising pups

The point of showing, remember, is to assess breeding stock...
In short, if you just want to choose a show dog for the sake of showing (and winning) then I think a dog is a better overall bet than a bitch. But if you have no intention of breeding your bitch, then she probably has just as much chance of winning as a dog. But if not for the purpose of assessing fitness for breeding, one would have to wonder then, why bother to show...?