Emojis in the subject of e-mails are not visible, instead a rectangle replacement character is shown.
This could be an error from your server. Who is the provider?
My provider is Infomaniak.com, but the same mails work pretty in Thunderbird, the Webmailer, AquaMail on Android and Outlook.
As you have discovered, not all email clients are equal, and eM Client is not very tolerant of misconfigured servers. Fortunately you have other options were it does work as you expect. 
What makes you so confident about a misconfiguration of the mailserver of my provider’s mailserver? Do emojis in the subject work in eM Client with others servers?
Mostly they do appear correctly. Here is an example from eM Client with a Gmail test account Junk folder:
So they look just fine.
But there was one thread on this forum, which I can’t find right now, with a similar issue and an employee from eM Client commented that this was because there was a mis-configuration on the server, which provides the header (To, From, Subject) that you see.
It is possible to recreate it by sending the same message, with the same emojis in the subject, to two different servers. Say one to Infomaniak and one to Gmail. Then add both accounts to eM Client and receive both messages. If it is a server issue, then the one will be displayed correctly, and the other from the suspected server will not.
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!