Hi Styczyński Mateusz,
Thank you for reaching Microsoft Community. I understand that you are experiencing an issue with your Surface Pro 9 SSD running at PCIe 3 speeds.
May I know where did you see these speeds? If possible, please provide us with a screenshot or photo of what you are seeing on your Surface.
Also, do you have the Intel i7 version or the Intel i5?
To troubleshoot the issue, kindly try first checking for the Surface drivers' health through the Surface app and run the Surface Diagnostic Toolkit to run some system checks and updates. Make sure also that all updates are installed in Windows Settings > Windows Updates including Optional updates then see if the speed improves. See this page for reference: Fix common Surface problems using the Surface app and Surface Diagnostic Toolkit - Microsoft Support
Kind regards,
Marrion