I want to create an effect using opacity, so I have to objects of identical shape exactly on top of each other. Is there a way to select them both and merge them? (As the top one cover the bottom one, I can't "see" the bottom one to select it.)

You can select objects behind other objects with Alt + click, then hold Shift to add the top one to the selection. Or you can use the XML editor (Shift + Ctrl + X) to select hard to see objects.

I'm not sure what you mean by merging though, you can union (Ctrl + +) or combine (Ctrl + K) paths, but if they're semi transparent you'll have to create a separate object and use the Dropper tool (D or F7) with opacity adjustments to make the new object "represent" the two older ones.

For selecting, you can also switch to Outline view. That will let you select objects that are otherwise obscured behind others. Once they are selected, you can switch back to the normal view if you need to and they'll remain selected until you select something else or de-select them in some way.

If the background object is sufficiently smaller than the foreground one, you can also drag a selection rectangle around it using - just make sure to keep the rectangle from covering the foreground object as well. Or let it select both, then shift-click to de-select the foreground one.