Assuming both clients are compatible with Hook and me and Mary are using individual and private email accounts.
If I send an email to Mary and later in another email I send her a link to that first email (linked from my sent items), will it work on her end?
As long as the mail app is compatible and uses the RFC5322 ID, it will work. Hook knows nothing about the actual accounts. It just deals with individual resources.
Just to comment that I find this works flawlessly. I use Postbox for email on the Mac, and have about 5 different email accounts. I exchange Hook links with others via email all the time, and either of us is able to use the same Hook link to open the email in our email client – wherever we’ve moved the email to!
P.S. The person you’re sending the Hook to only needs to have the free Hook Lite to click on the link and have it open the email in their account.
(This feels magical, but it’s not quite as magical as it seems. Every piece of email sent over the Internet has a unique RFC5322 ID. It’s just a question of whether the email app you’re using exposes that ID and makes it available to an app such as Hook. If you’ve selected your preferred email application in Hook, then it’s smart enough to find the email in your default application by using the unique ID.)
This feels almost like magic, really.
Unfortunately my counterpart uses Windows 
Yes, we’ need to release a free lite version of Hook for windows that can resolve email and hook://file/ URLs.