For those who doesn't know much about perl. Go to wakautils.pl looks for "# do <em>" without the "". Add this below:
# do <span class="spoiler">
$line=~s{ (?<![0-9a-zA-Z\*_\x80-\x9f\xe0-\xfc]) (~~) (?![<>\s\*_]) ([^<>]+?) (?<![<>\s\*_\x80-\x9f\xe0-\xfc]) \1 (?![0-9a-zA-Z\*_]) }{<span class="spoiler">$2</span>}gx;
replace the ~~ with what kind of trigger you want, and <span class="spoiler"></span> (note $2 must be there)
I personally doesn't know any perl and have just edited the line above it. From what it looks it works. As long as you don't do
~~something~~ and only ~~something~~.
Someone in here should know perl though and could make it work.