What is the best way to do to select the elements that make the bounding box area so big ?
I would translate that into "I want to simplify a layer to eliminate items far outside my area of interest."
This is a common task, for example, in the case of a small European country that may have island possessions far away from Europe. To take a historic example, Portugal + Macao. Opening a layer that has the country, one is surprised to see it zoom to the whole world. Why? Because a tiny area far from Europe is in the layer as well.
This is easy to do:
1. Click on the layer to be simplified.
2. Zoom in to the area of interest.
3. Select everything there using Ctrl-click and drag to draw a selection box that covers the area of interest.
4. Click Ctrl-I to invert the selection. You now have selected everything outside the area of interest.
5. Press Delete.
The above, of course, assumes your objects are not multi-branched. If Portugal + Macao seemed to be two areas but in fact were one, multi-branched area, then selecting mainland Portugal would also select the Macao portion as well. If you are dealing with multi-branched areas, first decompose to branches and then the above steps will work.
You see this effect frequently when working with maps of France, since France has so many overseas possessions. It's not just French possessions in the Pacific, it is also surprises like Saint Pierre and Miquelon just off the coast of Canada, so when you zoom to France you end up with the entire North Atlantic as well. :-) C'est la vie!