Your statement that minied code is only about variable naming is incorrect. While that's involved - minification also strips out any comments. Removes white space. And merges multiple files/libraries into a single file.
Also - it's becoming more common to have dynamically generated javascript. Which saves initial page load time, but increases the difficulty of understanding what the web application is doing.
Ie, your premise is wrong and would seem to indicate that you've never tried to work with modern minified (much less obfuscated) code.
Where the topic is up for discussion though is whether this matters or not. I suspect I at least don't care too much about this in practice. Other than javascript libraries, I have difficulty thinking of a javascript application that would make sense to contribute to or fork. Though I do agree with the general FSF argument that there's an increasing risk of users not having control of their machines any more as the market moves towards using only webapps.
Top Ten Things Overheard At The ANSI C Draft Committee Meetings: (5) All right, who's the wiseguy who stuck this trigraph stuff in here?