Q1 What proportion of computers have OpenGL and can interface with JOGL? (I'm suspicious because on some computers that I've run my Java2D game using the OGL pipeline there was no hardware acceleration). If OpenGL isn't supported, is my JOGL-coded game stuffed and won't display anything at all or will it work but at lower performance (ie will it fall back to software rendering, just not hardware accelerated)?
Almost all OS installations nowadays have some form of OpenGL. Hardware acceleration is available on all platforms JOGL runs on. If you code your game defensively and check before using functionality beyond core OpenGL 1.1, you should be able to run on really ancient machines. If you decide on a baseline minimum requirement like OpenGL 1.3 then you should be able to run on a fairly large installed base of machines while ensuring good performance and making life easier on yourself by not having to check for the availability of tons of functions throughout your game's rendering code.
Q2 JOGL seems to be changing a lot, its still a JSR and even some tutorial-example code doesn't work anymore because method names have changed. If I write something in JOGL now, is it likely to be runnable in a year?
Yes. The JSR-231 APIs are basically done at this point. It's true that a lot of changes have occurred over the past several months, but the current API set is unlikely to change at all before the JSR is finalized.