I always assumed the various tubes he sometimes has and sometimes doesn't have is due to the fact they are functional and exist in some configurations of his bio-weaponry and not in others. When you can shape-change yourself into your own arsenal, your appearance is likely to change over time constantly. Which is why I don't think there is any such thing as the definitive look of Apocalypse, and the artists that have drawn him over the years seem to agree. There are, of course, certain stylistic constants, but specific details are rarely the same for long. And that seems logically consistent with what the character of Apocalypse would be continuously doing: changing and evolving his appearance to adapt to his current situational requirements.
Incidentally, the fact that some of the images have the tubes and some don't is not a coincidence on my part.
