Will putting a camera SD card into my 3DS remove existing data?

I have used my old 3DS to test this out (because swapping SD cards on the New one is a pain), these are my findings:

1. I inserted a 32 GB SD card with about 5 GB of pictures and video files divided into 2 folders. The pictures are further divided into subfolders.
   
   Apparently, my 3DS could not identify the software on the card and thus refused to recognize it. The data remained untouched.
   
   

2. I inserted another 32 GB SD card, this time with a single .txt file with "test" as its only content.
   
   The 3DS did not complain. I then took pictures and looked at the contents of the SD card on my PC. The .txt file was still present, but now there were 2 new directories: 100NIN03, which contained the new picture and Nintendo 3DS.
   
   

3. As a final test, I deleted the .txt file and the 2 directories, and created a new directory called test.
   
   Again, the 3DS accepted the SD card without complaining. Back in my PC, the SD card reveals the test directory, as well as a new directory called Nintendo 3DS.

As you can see from my findings, it is possible that your 3DS will refuse to identify your SD card if there are still pictures on it, or files it does not recognize. However, it won't delete your pictures, at least not without your consent.

Note that the 3DS may have difficulties reading SD cards with 64 GB or more. The 3DS can only read FAT32 formatted cards, and cards with more than 32 GB are usually formatted in exFAT instead.

Assuming the pictures are stored on another SD card, taking out the SD card and changing it will not delete the pictures. It will though, make it so that you will no longer be able to view the pictures on your DS. Just put the old SD card back if you want to see them again.