I am told that the reason that the certificates and the logo were changed was because the WTF and KTA changed their logos, and so the new Kukkiwon administration wanted to change too. Personally, I do not believe that is a good reason to make changes. I don't know how many of this board watch Boardwalk Empire on HBO, but in that show, which is set in 1920, you can see the Coca Cola logo and others which look exactly like how they look today. The new WTF, KTA and Kukkiwon logos any sort of significant meanings that were embedded in the older logos.
The three different older logo of the KTA, WTF and Kukkiwon represent the five original kwan which united to form Taekwondo. The KTA logo, which features a fist, is the same logo which embodies the Chung Do Kwan, Song Moo Kwan and Moo Duk Kwan logos (and the ITF logo if you want). The WTF logo is modeled after the Chang Moo Kwan logo, with the two horses up on its hind feet, and the Kukkiwon logo was a series of Jidokwan otugi or snowmen in a circle.
The new KTA, WTF and Kukkiwon lack that type of embedded meaning. Some would say they don't have any meaning behind it.