The high pass filter is good for removing low-frequency noise. The most common example of this would be a switch-mode power supply, which usually runs at 50-500 kHz - hence the 500 kHz HPF. The low pass is good for cutting out high-frequency spikes. For example, if your target has other peripherals occasionally running, the LPF might help to cut these out. The LPF is also particularly useful for fast hardware crypto (especially because the ChipWhisperer is synchronous). For example, when every AES round is only 1 clock cycle, it’s hard to use a digital filter to clean up 4 ADC samples - this needs to be done in hardware.