What's interesting, from a balance perspective, is that bypassing armor is functionally equivalent to shooting through armor assuming you hit in both cases. You either lose the dice on the hit roll, reducing net hits or your opponent gets to add armor to his soak, generating (statistically) the same number of hits and reducing your net hits by the same amount. Because of the reduced chance to hit when trying to find a chink, there's no good reason to try.
This is true. If you crunch the numbers there really is absolutely no reason to ever make a called shot to bypass normal armor. It's functionally useless.
However, against hardened armor... oh wait, all hardened armor is natural these days (in 4A), which I believe can't be bypassed. Hmmm, ok, so, I can't find it in the books handy this exact second, but I would say if natural armor can be bypassed with this called shot rule, then it is useful against hardened armor (only), but if you can't bypass natural armor ratings then the option is bunk.
Now, that being said, you could cut the penalty for bypassing armor in half, giving only a -3 modifier to ignoring an an Armored Vest (6/4) as per your example, but as Kot mentioned, the penalty isn't only about finding the chink in the armor, it's about conditioning and overcoming said conditioned response/action. I suppose though to simplify things you would want to ignore all that and just focus on the "finding the hole" bits. You could add the ballistic and impact ratings of the armor together and then divide by 2 to calculate the penalty, so the Armored vest would be a -5 ((6+4)/2).
Or, you could offset the penalty incurred by comparing it to Reaction or Agility, or even their skill rating. Like something along the lines of Strength based recoil compensation a la Arsenal pg.163, although scaled a bit. Something like "Reduce the dice pool penalty for calling a shot to ignore armor by the attacking characters Reaction divided by 3" (or Agi/3; or [Agi+Rea]/5; or Initiative/4; or whatever seems appropriate to you).
Since I basically just did stream of consciousness for that, I went back and double checked what I typed and I have to admit - if I were to choose one of these options to use in my game, I would pick that last idea there (ofsetting via Reaction/Agi/whatever). It seems the easiest to implement and also seems to be the best at fitting into the RAW, in spirit anyway.
Anyway, let us know what you decide, I would like to know.