I bought a card reader so that I can remove the SD card from my Mini 2 and download the files to my PC, without turning on the drone.  Can I just cut and paste the folders onto my PC, or should I move the files and leave the empty folders on the SD card?

You can do either. Missing folders will be recreated by the firmware in the drone.

Also, personally I leave the originals on the card and store the card when it is close to full and start another card.

There's no need to leave anything on the card.
Formatting it after copying to your computer ensures you start again with a clean, empty card.

Hello there dankirk. Good day and thank you for the inquiry as posted above the missing folders on the microSD card will be recreated by the firmware in the said DJI drone. Ibn addition it would be best to use a supported SD card of your DJI Mini 2 for compatibility and reliability purposes. Thank you.

Your choice, either works.  I prefer to copy to PC and then reformat SD card for a fresh start.  Hasn't failed me yet.  

It can work either way!

Yes, either way will suffice. But I highly recommend and external hard drive to store your drone images/vids.
Welcome to the "World of File Management"....