One agent for a CoreIQ API and a Hub project, or one agent per product?

Can one Gene agent call a CoreIQ API and a Hub project in the same conversation?

Yes. One agent can use every application you installed for it, including Hub projects and OpenAPI services. The MCP gateway exposes that agent as a remote endpoint. Keep the tool list to what the role needs. The agent discovers actions as summaries and loads a schema only for the next call. Split agents when the permissions differ, not merely because the products differ.