is it possible to disable SPI0 channel on Raspberry Pi 3 B (with latest Raspbian) and keep SPI1 in use? I would like to use SPI1 only (due to custom PCB tracing) and need to use SPI0 pins as GPIOs... All manuals and tutorials only mentions disabling SPI1 or whole SPI subsystem...
You don't really need to do anything apart from just use the GPIO.
If SPI0 is enabled those GPIO will be in SPI mode. If you set one or more of those GPIO to be an INPUT or an OUTPUT those GPIO will no longer be in SPI mode (and any SPI calls you make will not affect those GPIO).
In summary as long as you set the GPIO you use to be an INPUT or an OUTPUT you need not worry about them being affected by SPI calls.