The Kobo doesn't do links at all; I'm not sure about my BeBook. All the links I found were external links, so they wouldn't be useful on the BeBook, Sony, Cybook Gen3, or any other reader without an active net connection.
By the way, I noticed that what should be list-bullets near the end of part 3 (Important Notes) show up as •, and the apostrophe in Crohn's shows up as â€(trademark)... so there are some encoding problems. These are probably caused because you don't have this line in your <head> section:
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
I didn't try adding it and rebuilding the file....
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