Where did you get the esp32-s3-devkitc-1-n16r8v.json from? This is not standardized. So please show the content of this file.
Probably your board manifest has
"extra_flags": [
"-DARDUINO_USB_CDC_ON_BOOT=1"
This will “route” the output of the Serial object to the native USB port.
In this case you need to unflag the macro in your platformio.ini
build_unflags=
-DARDUINO_USB_CDC_ON_BOOT