The sound of the sword penetrating in its body shouldn't have been 'kaboom', ecc anyway, it was not a punch xD Anyway, it doesn't make any sound, but Doomsday seemed to have felt it since it 'yelled': "Rrargh!", and it stopped to recover. And it seems to me that when it is wounded, instead of losing blood, he emits 'poison', which is the same that Superman inhaled after he teared it apart.
About the fact that the last time Diana's arms broke and this time no there's a really simple explanation: the position in which they were when Doomsday hit her. In issue two she was on the floor, on a side, and had her arm extended. Doomsday hit them both up down. Since the position in which she was, she had no way to contrast that blunt force.
In Doomed instead she had her arms in front of her, ready for the impact.
The same blunt force has not the same effect, and doesn't make the same damage if it is applied differentely. This time the impact was different, and so was the effect.
And for how I see it, Doomsday attacked with its left arm, she avoided it and collided against it, so it didn't even hit her like during the first fight, it was Diana who hit it after avoiding the blown, and its yell instead of being because it was ready for the attack, could simply be because it was angry its first hit had missed. The 'shards' between their bodies makes me think there had already been an impact.