Custom Emojis normally are a byproduct of the culture within the company. This can be inside jokes, meme culture, etc that the culture of the company dictates. Some emojis could be made from colleagues who agree to it within a company setting but not outside the company itself.

Since you can invite Guests to the Mattermost server there should be a setting that allows or disallows Guests from seeing custom emojis.

• A option in the Guest Access portion called 'View Custom Emojis as a Guests' (True/False)
• When true, guest accounts have access to custom emojis
• When false, guests only see the default emoji set (The one Unicode constorium sets)