How to detect what color theme AE is using via script?

Unfortunately ExtendScript doesn't expose the UI theme directly as a clean API call, but there's a reliable workaround that most script developers use:

You can infer the theme by sampling the background color of a UI element — specifically a Panel or Window — since AE applies the theme color to all native UI components. Something like this:

var w = new Window("palette");
var bg = w.graphics.backgroundColor;
var brightness = (bg.color[0] + bg.color[1] + bg.color[2]) / 3;
w.close();

var theme;
if (brightness > 0.5) {
    theme = "light";
} else if (brightness > 0.2) {
    theme = "dark";
} else {
    theme = "darkest";
}

The threshold values may need slight tuning based on your testing across the three AE themes, but this approach is solid and widely used in production scripts.
Alternatively, if you're building a CEP panel rather than a pure ExtendScript window, you have access to __adobe_cep__.getSystemPath() and the full CSS theme variables Adobe exposes via --color-bg and similar tokens, which gives you much cleaner theme detection without the sampling workaround.
Worth noting — if your logo works on a transparent background with enough contrast margin, you can sometimes sidestep the whole issue entirely.