1. Most Wordpress theme developers use popular Javascript libraries, so it wouldn't be too difficult to replace them with the original if you suspected something was amiss. The function wouldn't be a problem, if there wasn't any base64 code.
2. url() references should all be relative, in the same domain, so if it linked on the outside, I'd change it.
Most of the time I use a Wordpress theme as a starting point, rewriting some parts and looking over all of the code.
Also, mentioned above, securing the theme against injections and XSS is important.
1) Anything linked outside of the domain. 2) Anything not HTML/CSS/image/Wordpress tag/Javascript libraries 3) Anything encrypted.
Let me know if I missed anything.