All right I'm gonna try explaining this best as I can, so hang on for a moment
So suppose you had a completely normal non-hacked 3DS, yeah? You have a couple of games on cartridges and a couple of eShop games
When you pull out the SD card, your eShop games don't show up on the home screen. This is because they aren't stored on the NAND (a chip inside the system), but on the SD card in the Nintendo 3DS folder. Same applies to the save files of the eShop games, they're not on the NAND, they're on the SD. (The only exception is DSiWare games, as those are on the NAND) Retail cartridges however, would be fine as the saves are on the cart themselves.
Now when you create emuNAND it's the same, except it isn't using the NAND inside your console, it's creating a hidden partition on your SD card that you can't open and view the contents of, which pretends it's the NAND chip inside the console.
When you use emuNAND tool to create a backup, it extracts the contents of this hidden partition/fake NAND and backs it up in a .bin file. As with the previous example, the saves are just in the SD card contents. So emuNAND tool has no bearing whatsoever on the save files nor the games that you previously had installed as .CIA .
You with me so far?
All right, this means that before you perform a system format on emunand, you need to have done two things:
1) Use emuNAND tool to backup your emuNAND (sounds like you already did this)
2) Copy paste all the contents from the SD card to somewhere safe on your computer
Did you do just 1, or both 1 and 2? If you only did 1 then I'm afraid your saves are gone