when I did it, I did pull the whole assembly out, I think because of how the LS's system is shaped that not doing so would make it kinda hard.
for at least my LS, I have the one piece system with three cats, one off each header and then the larger single changer cat in the center, if the tool for hollowing was made with something that had a flexible shaft, they you may be able to go all the way through the third cat and then around the two bends to make it up to the main cats on each side.
the tool I had available was just a drill mounted paint stirrer, with a straight solid shaft and way only about 18"-24" long, also I wanted to be able to see down each end to make sure that all of the material was completely removed as I didn't want to leave a small amount that would just get knocked loose as some point and then get trapped in one of the mufflers.
if I ever pull do any changes to the system, I really want to actually cut the cat housing out and replace with straight pipe, I cant imagine having the pipe expand so much and then drop back down to normal size has to have some kind of negative effect on the flow since there is no longer the added resistance that the honeycomb adds to the flow.
if my cats were not destroyed, and I still wanted to go cat-less, I would probably definitely just make a new section of pipe to replace the whole assembly (especially with the resources you have available) so that I wasn't destroying such an expensive part that didn't have any problems!