For FPGA-in-the-Loop, you can set the clock frequency of your design. This is done in the filWizard if you are using your own code, or in the HDL Workflow Advisor if you are generating HDL code using HDL Coder. The maximum clock frequency you can set is 200MHz.
Also, please note that FPGA-in-the-Loop is a closed-loop simulation tool. The data exchange rate between MATLAB and FPGA is different tan the clock frequency, as the former is typically much smaller.
Also, I'm curious how you use FIL to control the LEDs, as we do not expose any external interfaces for users to use.