Does anyone know if this or other NanoPis would cause emissions problems if incorporated into a commercial product?
You will need to do some pre-testing yourself to determine that as the boards come without any certification. They are considered development boards and because you are likely to add additional items to them, you have the ultimate responsibility to ensure they meet the emissions standards.
I am assuming because you are asking about CE marking, you are looking to commercialise them? In that case, a spectrum analyser to cover the bands needed for testing is reasonably priced these days. The Rigol DG815 covers 9Khz to 1.5Ghz and is a good low-cost option. Along with a LISN and some good EMC probes you can set up a decent enough test bench for pre-compliance testing.
This Youtube video from the eevblog is a really good quick introduction to testing with the Rigol DG815. The second one covers using a set of EMC probes. He rambles a bit but the information is well worth watching. https://www.youtube.com/watch?v=uLIr1eFjY2shttps://youtu.be/CQgJmmn-eSE?t=1667