The routability of PSOC is not perfectly general, there are constraints, discussed
in these docs -
http://www.cypress.com/documentation/application-notes/an86439-psoc-4-using-gpio-pins AN86439 - PSoC® 4 - Using GPIO Pins
http://www.cypress.com/?rID=39677 AN57821 - PSoC® 3, PSoC 4, and PSoC 5LP Mixed Signal Circuit Board Layout Considerations
http://www.cypress.com/?rID=102505 AN94020 - Getting Started with PRoC™ BLE
http://www.cypress.com/?rID=102504 AN91267 - Getting Started with PSoC® 4 BLE
Curious, what were you driving externally that caused device damage ?
The pins are made "hidden" because they are associated with a dedicated IO-port which is not changeable. Setting the pin's properties (as far as they do not conflict with the component's requirements) can be made using the definitions made in the component_pins.h-file, just have a look into that.
Is there a way to create schematic objects for these hidden pins so we can connect them to other PSoC components?
The datasheet describes them as "I/O connections buried (not exposed) at the symbol level"