There is a possibility to update contacts and import link to a company without email/domain using a third-party solution, such as Import2 Wizard. There, you can use any field on contacts to match, such as “name” or “ID” - or, even by custom fields if you wish.
Here is a short video overview on how to connect a contact to a company using “name” as a lookup field in Import2 Wizard: https://youtu.be/NP27PDeCYJU
Also, Hubspot released an update recently so that you can update/import records using Contacts ID: https://www.hubspot.com/product-updates/now-live-import-deduplicate-and-search-objects-using-object-id