I did some testing with different mailservers, senders and so on and it turns out:
eM client just doesn’t show all emojis. You can reproduce that with a subject containing a yellow circle U+1F7E1 (Unicode and Emoji 12.0) and a red circle U+1F534 (Unicode 6.0, Emoji 1.0): The newer one is shown as arectangle-placeholder, but the older one with a monochromatic representation of the red circle (at least round). So the problem are in fact two: The emojis are monochromatic, but the color may be important, and very new ones haven’t fount their way to eM Client yet.
Both are acceptable while not quite graceful.
Thank you for your reply!