500 MHz CPU runtime operation is supported if it is achieved by the CPU clock divider / cpufreq path, not by lowering the CGA PLL itself below 1 GHz.
For the PCIe abnormality: if the frequency change is done through the normal CPU DFS path, NXP evidence says only the CPU frequency is affected, while AHB/APB remains unchanged . Therefore PCIe should not be impacted by CPU DFS alone. If PCIe becomes abnormal, check whether the implementation is also changing platform/SYSCLK/PLL ratios, because the datasheet requires the platform clock settings to remain within their valid limits and states a PCIe platform-clock requirement for proper PCIe operation.
LS1043A does support runtime CPU frequency scaling to 500 MHz, but the CGA PLL must stay at ≥1 GHz and PCIe/platform clocks must not be disturbed.