Many buses used in industrial control equipment such as CAN bus and Modbus do not use encryption. I suppose there's more risk if you're using TCP/IP and connect laptops that have been online to the LAN, because it's such a common protocol.
But again sophisticated malware could just wait until you have your USB CAN dongle connected to the laptop, and still attack the CAN bus. Heck, CAN bus and Modbus don't even have any password protection at all.
I've never heard of this being used with really low-power embedded stuff, but if you stretch your definition of embedded to the point where you include things running stripped down Linux, this is a pretty viable setup if you have those devices distributed across a LAN with a managed switch in the middle.