Regarding 1, you're right, but it's a critical issue for now. I've filed an issue related with this, please see the following issue for more information.
Regarding 2, I'm not sure about this. There're a few JavaScript code within results of YUIDoc, but it seems to be of modest size. Anyway, I think we should take a look on this if that is a problem.
$ ls -l out/assets/js/*.js
-rw-r-xr-x 1 okuryu staff 1445 4 9 20:33 out/assets/js/api-filter.js
-rw-r-xr-x 1 okuryu staff 6568 4 9 20:33 out/assets/js/api-list.js
-rw-r-xr-x 1 okuryu staff 2924 4 9 20:33 out/assets/js/api-search.js
-rw-r-xr-x 1 okuryu staff 10297 4 9 20:33 out/assets/js/apidocs.js
-rw-r-xr-x 1 okuryu staff 482 4 9 20:33 out/assets/js/yui-prettify.js
-- Ryuichi