Ok, so I was egg farming for a shiny scorbunny and found one, but then I realized..."what do I do with all these scorbunnys?" so I just have 1000 scorbunnys filling up my boxes, what do I do with them?
Assuming you do not want them: Apparently, the fastest way to remove Pokemon from your boxes in SW/SH is to view them in Pokemon HOME, (either mobile or Switch) from where you can mass release Pokemon at a max of 100 at a time.
Source 1 Source 2: Various Reddit posts