I am going to say YES. Security through obscurity works if you're more obscure then your neighbors :) (joking but there is some truth to that).
The reality is that the bots/scanners now compile the plugin lists right off wordpress.org and crawl the plugin url's directly, fingerprinting versions for known exploits and keeping the info in a database for reference.
So which one would you rather have, a bot not being able to gather info on your install, or leaving it up to the plugin author to make sure you're secure. How about both.
ps. On a side note there were 186 reported exploits from wordpress.org plugins last year .(*reported..).
Options –Indexes
in the bundled htaccess, so these files wouldn't be necessary...