I have used WooThemes in the past and personally I think some of their code and their modifications are a bit overkill, sure it makes things easier for users but its not really following the way WordPress does things (Creating folders in WP-Content to put file uploads from their admin panel for example).
In general terms I think its better to hard code references to public resources (CSS Links, JavaScript links etc in header.php). For better speed increases I would suggest having links to JQuery or MooTools in header.php and any other JavaScript files should be put in footer.php just above the closing body tag.
The benefit to this is that the core JavaScript framework (JQuery or MooTools) is loaded first, the page can then render on the screen whilst the last few JS files are downloaded and put to use.
It maty be worth using WP SuperCache or similar to cache your pages and allow browser gzip compression for quicker page loading.
I think WordPress in general makes too many database calls anyway, so where possible I think its acceptable to hard code links.