You can do this in conf/userstyle.css -- if it doesn't exist create it. There you can define your own css for unordered lists.
See:
http://www.w3schools.com/css/css_list.asp
Preface your definitions with .dokuwiki, as in:
.dokuwiki ul
{
list-style-image: url('http://your_site.org/path-to/empty_box.png');
}