STM32 GPIO Speed

STM32F4-Refrence Manual in page 278 says that "The data present on the I/O pin are sampled into the input data register every AHB1 clock cycle"

This text is referring to input pins, not outputs.

The output speed register only affects pins which are configured as outputs. It controls the slew rate (drive strength) used for the output. Using an excessively high speed may cause ringing and EMI on outputs, so it is important to use the minimum speed required for your application.