Thanks Joel! I came across the thread you referenced while Googling my problem, the thing is, I do not know how to tag URLs that are not included in the text itself, and have been unable to find any information on how to do this. Does this mean that I would have to copy each URL and insert it after the link text (manually (ugh!) or with a script)? This is precisely what we want to avoid, since we want to keep the text readable - with up to 30 - 40 links in one 2,000-word text. Or is there a possibility to copy/paste the URLs in the XML data, but not in the text? Thanks again in advance!
Well, yeah, it means manually, or with a script, but not manually like you mean. It's worse, actually; you'd have to go to each URL element in the Structure pane, and add the destination there. You'd need to add a new Attribute in the Structure panel. Right-click on the URL element in the Structure pane, choose "Add element..." and then add a destinationURL attribute with the contents of your link. So it'd wind up looking like this onscreen:

That's actually more clicks, I think, then trying to do it by hand in the XML output! But it's not hard to imagine a script that
1) runs through the doc until it finds a tagged URL that has no destinationURL attribute
2) extracts the Hyperlink Destination from the Hyperlink
3) adds a destinationURL Attribute to that tag
4) adds the hyperlink destination extracted in 2 above to the Value for the freshly created Attribute
or something along those lines. Depending on the total volume of links to process, and the frequency with which you'd have to re-do this work, it might make a lot of sense to write that script. Honestly, if I didn't have hundreds of links to process, I'd be inclined to use AutoHotkey to make the copy-Hyperlink-Destination-from-InDesign-and-paste-into-Notepad++ action into a single keystroke, but that's because I feel like it'd be faster for me, personally. (I stumble through old-dialect Javascript quite slowly, but I feel like I can automate a repetitive copy/paste task in AutoHotkey's scripting language in just a few minutes.)