There isn't anything in beta currently. Secondary domains are tricky since they're not just a list of values, they reflect internal identities. This makes a public API more difficult than just read/write access to a property. I'm not currently aware of any plans to open a public API for managing secondary domain.
Similar story for merging company records; because of the interactions with other object types (contacts, deals, etc.) merging companies is slightly more complex than merging contacts. I'm not aware of any plans for a public company merge endpoint.
To avoid duplicate companies (where duplicate means the same domain), you can use the 'Search for companies by domain' endpoint to check for existing company records with the domain you're looking to create.
Additionally, I can see the use case for a public endpoint that deduplicates based on company domain. If you have the inclination, I would encourage you to check out the Ideas Forum on the HubSpot Community. There, you can create a post including your use case that product and other customers can see.
It's not currently possible to add secondary domains to company records via the API. The only way to have company records with 'secondary' domains is to merge two existing records.