In my experience, there is absolutely no problem whatsoever with this sort of thing. Bare populated circuit boards are easy for the x-ray folks to inspect, in fact they will look similar to familiar packaged electronics since the case is generally almost invisible to X-rays. I quite often travel with this sort of thing (prototoypes, evaluation boards and so on) and have encountered zero problems, not even any evidence they looked into the bag. They can see there is no danger.
Do not put batteries in checked baggage especially in home-made electronics, and never lithium cells. I'd also be a bit careful about weird looking bare or home-made looking electronics in carry-on, just because it might freak out another passenger if they happen to see it (perhaps whilst you are accessing your in-flight cache of snacks) which you do not want to do.
The only thing worse would be to pull out your Arduino with flashing LEDs and start plugging it into your laptop to get a bit of programming done in-flight.