You may observe the pll_locked signal to be always low in SignalTap® II tool, if you have selected an incorrect signal from the netlist. When adding GXB transceiver lock signals into SignalTap II file, there are more than one choices: pll_locked and pll_locked. pll_locked node should be selected. In hardware testing, pll_locked is always low.
pll_locked is a bus name, which should not be used in Signaltap II. You can confirm the connectivity in Quartus® II Analysis & Synthesis report. In Analysis & Synthesis report file, there is a section called In-System Debugging. This section shows the actual connections made by Quartus II software. You will find that pll_locked is a missing node and connected to GND. pll_locked is a properly connected signal.