The attack on Ordon village and the Wolf sneaking in the night looking for a sword and shield are one of my favourite parts of TP plot, so I did give it a thought while I played. That's what I think:
Link transforms from hylian to wolf in the very hands of a Shadow Beast, having the triforce shining in his hand and everything. I don't have a high opinion on the shadow beasts -since they are twilis transformed to follow orders blindly and in battle they look quite mindless. So, I believe the shadow beast that had Link thought he was a strange creature and maybe his master would want it alive -but he didn't know better. hances are Zant didn't even get to know there was a wolf imprisoned in his dungeons.
The children are a bit more complicated. It could be just something that happens on wars, like said above: either ensuring the village won't raise arms against Zant by capturing their children (really unlikely), or just the bublins enjoying brutalizing peasants, in a children-rated Zelda kind of way: now that Zant is king of hyrule the bublins don't need to fear the soldiers any more and can do things they enjoy like that.
But why so soft damage? Why don't just kill everyone and set the village on fire? Remember what happened to kakariko and to Zora's domain. Kakariko was a rather large and prosperous village, and judging by the houses we could say around 40 people lived there -of whom only three survive; Renado, his daughter and Barnes. The Zora's had their queen executed, and then their whole land was cursed with ice and cold.
If we take the Ordon raid as the standard was to attack springs, we see that firs comes King bublin with some backup to summon the shadow beasts, and then the dark ones come and tear apart the light spirit. Since the attacks on ZD and Kakariko are much worse than in Ordon, where it was incomplete, I'd feel inclined to think it's the Shadow Beast's who do the most damage (we actually are told that in kakariko the shadow beasts massacred an old woman and some men, if I remember it right).
So maybe the Bublins were aiming to create a bit of confusion before the shadow beasts came and slaughtered everyone else. That's Twilight Princess for you. You know, for kids.