Gateway will not automatically delete your data. However, when you use the format emuNAND option on the Gateway menu, it wipes all of the files off of your SD card except the Gateway launcher. Before formatting emuNAND backup the contents of the SD card. After your format emuNAND replace them on the SD card. If you haven't actually purchased the Gateway yet, I would recommend going with CFW instead. It can do almost everything Gateway can do (some of the CFWs actually have features that Gateway doesn't), it is free and it has the ability to coldboot. If you don't have Cubic Ninja or Ocarina of Time, you'll need CFW to set up Gateway anyway, so might as well skip on the Gateway cart.
Thank you for the advice! This may sound stupid but I'm just trying to play it safe as the 3DS in question here is not mine, so backing up the SD card and restoring the files will keep Miis, streetpass, etc from being lost?
Thanks again!