I never ran into this problem, but now I did, after working with Solidworks for two years:
How do I cut a hole or another kind of extruded cut through an entire assembly?
Just like you would cut a hole in a part. Create a sketch, cut though all.
As for the shell question, you can use a surface fill to patch the hole in the shell.
In Assembly Features, you can make a cut very similar to making a cut in a part, and you will have the option of having the cut apply only in the assembly, or have it edit the part files.
For patching holes I am a big fan of the "Delete Face and Patch" tool. If you are talking about surface bodies, I use either "Delete Hole" or Untrim.
Retrieving data ...