A recent discussion on the forums about Thunder Clap and its being suppressed by silence effects (it always has, or at least has for so long that I've just accepted it) brings out Ghostcrawler to explain the reasoning. Quite frankly, it's a pretty reasonable explanation: if you're silenced, no one can hear the Thunder Clap going off, and thus, it doesn't do anything.
It's not due to the ability being magical or not, silences prevent spell casting by preventing the spells themselves from being uttered, they're not a dispel, so it makes sense in game that silences also prevent any other ability that needs to be heard from working. I know from tanking Raging Spirits on top of ICC that I also can't taunt when silenced, which makes sense. I can yell all the insulting words I want at the ghost, but he can't hear them. I'm honestly not sure if I can Shockwave in this situation (we have very fast dispellers) but some sources I've checked indicate that yes, Shockwave is also prevented by silence. (I really don't get silenced all that much. I'll run some tests later today.)
I find it very interesting to see the complexities of how abilities and conditions interact in game, and how abilities are changed by in-game world logic. One class obviously uses the Holy Light, while another is just getting by on brute force: the in game distinction creates new complexities.