You can ditch the hardcoded target
attribute, as you intend to add it via the js anyway. Also, once the js function has done its thing, you want the browser to act upon the new href, so you need to return true, not false.
(Alternatively, not returning anything has the same effect.)
<a href="#" onclick="updateLink(this,imgArray[x]);">
obj.href='index.php?hitCount=1&linkID=' + linkID;
(In case you hadn't done so already, you should consider what non-js users get out of this link. If the content is essential to the site and not strictly js-related, then you should try to make that content accessible to those without js.)