I think I found my answers:
"Here's a guess: During the initialization phase of a Johnny-Five/Raspi-IO application all available GPIOs on the Raspberey Pi are automatically configured as GPIO outputs, irrespective of whether the Johnny-Five/Raspi-IO application actually use those GPIOs or not. On the other hand, node-red-node-pi-mcp3008 requires that the SPI specific GPIOs be configured as SPI GPIOs, not as GPIOs outputs. They were actually configured as SPI GPIOs at boot time but the fact that Johnny-Five/Raspi-IO reconfigures everything to be a GPIO output then breaks node-red-node-pi-mcp3008."
Here's the link to the thread: