AFAIK in my game, I've been playing it that pen goes straight through toughness bonus as well as armour. Possibly my players (who to be perfectly frank know the rules much better than I do) have been playing it properly, it would account for some of the disparity that happens in fights. However it seems to fit to me that the Pen should tear through flesh and armour equally.
As to the Horde rules, I was doing this anyway. The stat blocks for individuals in
DH/
RT/
BC suffer the "3.5" problem of being basically the same as a player character, meaning I as a
GM have to remember a lot more stuff and have to think carefully about everything. That's fine if I have prepped it properly, but the nature of my campaign as a totally open sandbox means I can only really prep once the guys have gotten their teeth into an endeavour- there is usually some stuff at the start of any endeavour where they do something unexpected and I have to ad lib. Which is perfectly fine and I enjoy it, but it means running complex enemies out of the book with little prep time. I feel this makes them much less dangerous and effective. For that reason I focus on the big bads and villains and abstract the various minions and so on. They have wounds and damage soaks but it's all pretty abstracted and I also abstract their stats and damage to a degree. I know my players read this forum, so I'll also say that I do not abstract important villains or major threats in this way

. And I am consistent with how many wounds or soaks I give the other guys. The horde rules seem like
FFG's nod towards this sort of thing that I am sure plenty of
GM's do anyhow, and just giving us a quick and easy way to do it.