This is one of those questions that seems really difficult to answer but I feel like it’s really easy to answer.
For one, we can quite easily assemble enough atoms to be visible and to interact with light and then look at the color that comes off of that, so in that instance yes atoms do have colors.
Colors are, after all, fundamental consequences of our perception of the electromagnetic frequencies of a very narrow band of the electromagnetic spectrum.
Do they tho? A single atom is too small to have an actual “color” I believe, and if you arrange them differently you’ll have different colors. For example, carbon arranged like a diamond is clear, but carbon in coal is black.
The carbon case is that light passes by, it’s beyond me but that comes down to molecular structure and not individual atoms.
Atoms actually have color, just not one. Atoms have these electron orbits, if an electron gets hit with the right energy (which is actual discreet energy levels) the electrons can jump to a higher orbit. It can then fall back, and emit light of a specific wavelength corresponding to that energy difference. It’s how spectroscopy works, by testing all visible colors of light (and probably outside visible spectrum too) you will get dark areas in the color band where said light/energy was absorbed.(because the emitted light of the same type that hit it goes off in random directions)
Each atom will therefore have a unique color strip for identification, so we can say atoms have colors!