Hi. When using email.send, you can specify recipients by passing an array of contact internal id's. Does this separate based on company? i.e. if contact A is a contact of Company A and contact B is a contact of Company B (with company A as a parent) - does it send 2 emails, one to each contact? I have this situation at the moment, and suspect it is doing this but cant find any documentation on it

I don't believe it does any kind of filtering it just sends one email with all recipients in the "To:" field. You should be able to test this in a sandbox though.