Seems like the include folder was removed but the code in the PIO builder script was not removed.
A fix is proposed in Remove tools/sdk/include/nimble from include path by maxgerhardt · Pull Request #4891 · espressif/arduino-esp32 · GitHub.
Otherwise the warning can be ignored.
If you want a fix now, you can do the code change in C:\Users\<user>\.platformio\packages\framework-arduinoespressif32\tools\platformio-build.py and Ctrl+Shift+P → Rebuild IntelliSense.