Yes, that's an unfortunate "feature" of the terminaljs component we're using for output. I railed against this limitation myself a couple months ago, but it's not something that's easily fixed; fundamentally it's all down to HTML's standard behavior of treating all whitespace runs as just a single character.
To fix it properly, we'd need to throw that out and replace it with something else — but our searching didn't turn up anything better, so it would probably mean writing something from scratch. And I'm not really in the business of making JavaScript components. 😛 If this is an area where you have some expertise, I certainly wouldn't turn down some help...
Note that if you use command-line MiniScript, or Mini Micro, printing a blank line works exactly as you'd expect.