I’ll vote in favour of finding a way to add multiple email addresses. 
Until then, though, a couple of points…
It’s a kludge, but what I do is just let the CRM create a new contact. When I see someone that I know is an existing customer at the top of my contact list, I know what’s probably happened. It takes 2 seconds to merge those contacts, and end up with all of the timeline information in one place.
Second… I’m a tester for the android version of the app. One thing I’ve noticed is the exceptional responsiveness of the dev team. For all the above posters that are feeling discouraged about Hubspot over this less than perfect functionality… I wouldn’t worry too much. IF there is a way to accommodate us, I’m sure it’s in the works.