Yeah, you have to switch to TPS mode (Tab on KB/M or LB on controller) to shoot the weak points on the zombies. I thought it was a really clever idea at first but it turned out to be really clunky ^_^;
The good news is you don't need to see the targeting symbol to hit the weak point; you just need to remember where it is. But you do have to tag it with the scanner at least once, though!