STM32F4 HSE clock frequency without HSE
On the Nucleo board you can drive the HSE from the STLINK clock (just choose the bypass option in your cubemx.

It is possible in some circumstances that the HSE can be driven by the bypass clock even if the pin is not configured properly. 

To check it step through the clock startup routine (using the debugger) and see if the HSE clock has started properly. Then you will not have to guess.