Whatever you were reading, was wrong. JCing is #1 for rogues, it is however very expensive to level up, as well as ENG.
Most good Sub rogues will gem for Agility. There is a Crit Cap that you will want to hit, I think its somewhere around 32-37% for PvP, then after that you go for AP. I on the other hand in 3.3.5 Gemmed for Stamina + Key trinket from PvE badges. had somewhere in the neighborhood of 37000 HP unbuffed with still a 75% crit on my Ambush.
Its all a matter of preference, but if your playing Sub Correctly, then you will need to hit your crit cap, then follow it up with whatever stat you want. Armor pen is not valued highly for Sub as your damage will be Bleeds + ambush.