Universal binary is a file format for executable files, not a certification program.
A universal binary supports multiple architectures, e.g. PPC and Intel, in one file. When a program is shipped as a universal binary there are not "two copies of [the] program in each box." There is one copy that can run on either architecture.
There is a universal logo program for promoting software delivered as a universal binary but that shouldn't be confused with what a universal binary is.
Apple's Xcode development tools support building universal binaries. It's a build configuration option in the Xcode UI.
Generalizations about universal binary uptake among software vendors can not be made based solely on Adobe. Many developers were shipping universal binaries for months before the January MacWorld Expo.
Adobe's Mac OS development is tied to the Metrowerks tools. Metrowerks is now part of Freescale and doesn't appear to even offer Mac OS X development tools anymore. To ship universal binaries Adobe first needs to migrate from Metrowerks to Xcode.
Metrowerks was a hero in the 68K to PPC transition but in terms of Mac OS support they have been in decline for a long time. I'm sure there are other vendors in the same situation as Adobe but I'm also sure there are many more that recognized Metrowerks' decline and heeded Apple's advice to move to Xcode.