Currently, changing opacity on clipping masks doesn't seem to do anything. It would be extremely useful to be able to set a clipping mask to different opacities.
For example, I was working on a map where a flood is taking place and and I wanted some downed trees to be partially submerged, so I tried putting a clipping mask on them and setting the opacity to 0.5. It looked the same at 0.5 as 1. Nothing changed until it was set to 0, then it disappeared.
Being able to change opacity would have broad utility for some really cool effects, like being able to blend things in and make something partially submerged in its background.