Still unanswered, is there a significant advantage to Reformat SD card before installing new CHDK version?
What I wrote above has nothing to do with updating CHDK, it's a generic advice

You can just copy the new CHDK files over the old ones, if you don't notice the card reading/writing speed being slow. I haven't done any tests either, but card writing/reading speed has nothing to do with CHDK (other than CHDK's ability to perform a test).
Do you have any test recommendations so I can keep it as a baseline for future reference?
You don't need to test this every time. Even the test might cause some minor fragmentation since it writes onto the card

" I also remember reading it in the Magic Lantern forums written by people who use high speed cards for their high bitrate video recordings." Do you have a link to this post?
Nope
http://www.magiclantern.fm/forum/