I've installed Q2A-Akismet-Plugin-v2b3, on q2a 1.6.2.
From my tests the option :
" Moderate questions/answers/comments that contain links when the user has less than X points"
works only when a link is inserted in the post (ask question form) using the CKEditor link button.
If the link is inserted directly (plain text) in the post (ask question form), without using the link button, the post is not moderated and a new question is published with a clickable link.
Do you have the same behaviour ?