From version 3.0 and onwards, working with logos in Refined has changed a bit.
Logos uploaded to portals in default Jira Service Desk project settings will only be rendered when using breadcrumb navigation and version 3.0.2 and up.
The main feature to the logos was changed in version Refined 3.0.
Uploading icons to category, projects and links
Icons can be added to categories, projects and links. An icon is used by the Site Navigation module. Please note that the site navigation module needs to be using the "cards" style for rendering.
Uploading logos to sites
Logos can be uploaded to Sites. When a logo is uploaded to a site, the logo will show up on all pages on that site