Zynq features four clocks, the FCLKs, which are routed into the PL. In a Linux based system device drivers are expected to be clock aware and take ownership of their clocks and gate/ungate and change frequencies on their own discretion. For these purposes Linux features the 'Common Clock Framework'. Please refer to Linux kernel documentation and sources for more information about this.
By default the kernel will disable all unused clocks to save power. Please make sure you have the below 2 configs enabled if you are not using xilinx_zynqmp_defconfig