Currently JAMSS searches for PHP based code only, so the JS malicious code won't be recognized at this time, but might get in future releases.
This script still doesn't do any cleanup on its own, it's only informative about some suspicious code in your Joomla! installation.
This script is far from being 100% accurate. It has just a few patterns at this moment, and the false-positives are very well to be expected. So you may only use it wisely and with caution. I do not take any resposibility for any damages you might suffer by following some advices or results of this script.
I am very glad JAMSS was helpful. Thank you for the review.