Ah, the "sit on a box" trick. Yeah, that's a good safe way of killing them. It can take a while, though, and I've seen some boxes being pushed by the dogs so it's not always safe.
Sitting on a box always felt a bit like cheating to me so I avoided it. I like the "right-click throw a barrel in their face repeatedly" tactic better
I used to wander around with a barrel in my hand whenever there was a dog in the neighbourhood.
Spoiler below!
That came in handy for the dog behind the locked gate where Red contacts you for the very first time, after the morse code bleeps that gave away the door code.
Someone should really make a mod for Penumbra that increases the enemies' hit points. Of course the pick-axe is necessary in some parts of the game, but it would make the game much scarier if you could not kill the enemies with ease. Running from the dogs is not impossible if you use some strategy, and would certainly add a lot of tension to those moments where the dogs spot you.
When I made my walkthrough for Penumbra: Overture back in the day, I played the game on Hard difficulty and didn't kill a one dog during the whole game.
Much more easier (and scarier) is sneaking past them than punching them in the nose. If you'llHAVE to use the pickaxe, use it once to knock the dog down and then run away.
I think the running should've been nerfed too, you could literally sprint all the way past them if you knew where you were going without being touched.