The texinfo manual even uses @acronym{GNU} as example. It's an example of how to use a Texinfo command. It doesn't necessarily mean that GNU manuals should use it. There are plenty of Texinfo commands which are there for "alternatives".
Do you have a rationale for eliminating @acronym? I've very very rarely seen it used in other GNU manuals. The Texinfo manual itself, for example, doesn't (aside from the description of the command itself). Emacs and GCC don't (last time I looked). Etc. Also, simplicity argues to remove it. Do we really want hundreds of '@acronym{GNU}"s scattered everywhere? Yuck. You might ask, why does it exist at all. The answer is, in non-GNU manuals, I sometimes wanted to print all-caps words in one point size smaller type, which is a common typographical refinement. However, GNU manuals don't do this. So I vote for the color "invisible" :). Best, Karl