I have a Perl script I wrote years ago to update all of my wordpress installations via FTP. It holds all of the login data in a flat file which freaks me out too. Like I said, it uses FTP which is almost obsolete these days but it worked well for updating a bunch of sites quickly. You'll also need the Net::FTP perl module installed. With my script you still need to manually visit each wp-admin to complete the db upgrade. If you're interested I will see if I can find the script. I probably have it on an external drive somewhere.
I pulled the plug on my blogs a couple of years ago and merged them into just a couple of sites. If I had to update that many again I would use something like Git or svn. Check this out:
http://deanpcmad.com/post/6532651808...-using-git-and