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Not directly, no; the SD card won't show up if you just hook your Switch up. However there are things you can do! There's a sysmodule -- basically, a piece of code that runs whenever your Switch is on -- called sys-ftpd that runs an FTP server on your Switch that you can connect to to move files back and forth. Or, you can use Hekate's USB access feature to accomplish the same thing.
You probably don't need to do a wipe of the SD card, but it wouldn't hurt. Do so after you dump the games using DBI. To wipe the Switch itself, you'll use a payload called TegraExplorer, which includes a SystemWipe.te script that will handle wiping the console.