I shoot my sonic emitter at the force fields in Old World Blues, but they don't go down. Am I doing something wrong?

Did you get the upgrade for the sonic emitter that gives it that ability?

Apparently not. I've got the Opera, Revelation and Tralantula. Tried al three.

The shield upgrade is apart from the others. Once it is installed, it stays with the weapon in addition to any of the others.

Yes. And you get it by doing the MQ. Specifically, the portion of the MQ that takes place in the high school with the robodogs.