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Do the respective planets in 40k have individual flags, like countries on earth today? If so, does anyone know where I could look at them? I thought it would be a neat little detail for a mixed-planet guard regiment like what I want to create.

Note: to keep it simple, for the purposes of this topic, lets use the Single Biome Planet trope.

Most planets almost certainly have some sort of heraldry they use. But their use beyond that planet's surface will be limited. Bureaucratically, the Imperium simply tracks planets by number and name if applicable.

Pretty sure there isn't any sort of official listing of flags and such.

I would assume so. I am sure many planets would still have regions whether they are former countries or city-states would each have there own flags. Just because they are part of the Imperium doesn't they throw out all they were before.

I don't think you are going to find much in visual representation in 40K art though. You would probably be better served just looking at different flags around the world taking inspiration from them. You could also look into medieval, Renaissance era heraldry for inspiration as well.