But it depends on your obfuscation, and it depends on the amount of code. Some obfuscation results in considerably larger filesizes -- which can increase overall pageload. It also results in slightly slower js code execution.
Both of those issues could in some cases, have a very slight negative effect on SEO, but it's unlikely to be an issue in most cases.
Perhaps best if you push your side through a Bot Simulator like this one.
Bottom line is - don't make your SEO dependent on JS.