The standalone 'markdown' utility is perfectly happy with an external link inside a `<h1>`, e.g.:

    # Review of [Dwarf Fortress][]
    ...
    [Dwarf Fortress]: http://www.bay12games.com/dwarves/

produces

    <h1>Review of <a href="http://www.bay12games.com/dwarves/">Dwarf Fortress</a></h1>

but when I try to use this construct in an ikiwiki page, I get 

    <h1>Review of [Dwarf Fortress][]</h1>

It works fine with h2 and deeper.  The square brackets also appear in the output of an [[ikiwiki/directive/inline]] directive in archive mode, I haven't tried non-archive mode.

> I think you were confused by markdown's slightly wacky mix of square brackets and parens.
> The url in a markdown link goes in parens, not square brackets. For example:

# [Google](http://google.com/)

> [[done]] --[[Joey]]