Add this before the </body> tag in an nvALT template.html file for working [[note links]] in the preview.

template.html

<script>
window.onload = function(e){
	var container = document.getElementById("wrapper");
	container.innerHTML = container.innerHTML.replace(/\[\[(.*?)\]\]/g,"<a href='nvalt://find/$1'>$1</a>");
}
</script>