I once designed a Battery Management System for an electric car prototype. There were a lot of peripheral PCBs that could be exposed to a mild to moderate environmental hazard.
Long story short: The CAN Bus didn't have any problem with the conformal coating. Heat management was tighter to prevent any thermal runaway (i.e. we lowered the max temperature rating and ensure that the circuit was not over the temperature rating).
The only Problem I had with conformal coated boards: you can't easily do field repair on them and you need to be extra careful with your connectors. You don't want to jam them in conformal coating or overexpose them. Enclosed connectors like Molex Microfit are efficient at that. You can even plug in a dummy connection to protect the inner part of the connector while you put your conformal coating.
Bear in mind that different coating may yield different results. Ours wasn't a particularely thick one. I saw once black conformal that was almost rubber like at the end and almost 1/8 of an inch thick...it was heavy duty to say the least.
Finally, when I apply conformal (don't know if you do it yourself), each layer is crisscrossed at 90 degrees. 3 to 4 coating did the trick most of the time. however, like I said previously, my conformal coating is on the thin and light side.