You can flash SuperSU from recovery (CWM or TWRP) to reinstall the su binaries again. You should then either have SuperSU already installed, or you can install another SU app. Then install Apphider again, grant it root, and then unhide SuperSU if it's not already showing. I ran into something similar yesterday while applying the OTA to a rooted Nexus 5, and this fixed it.
