Is it natural that every time I create a backup of nand of my 3ds xl using Gateway, it will have different MD5 Hash from before???

Also to answer your question about 6.x eShop games, I had the Omega Ruby/Alpha Sapphire Demo running on 9.x before downgrading and was able to keept my save file. So I don't think you should have any trouble.
The downgrade doesn't format your sd card,but if you haven't done it yet, you should setup your emunand before downgrading.

Yes you can use your sysNAND backup to restore your emuNAND to 9.2 with the emuNAND tool.OK, Thanks.And, Can I use my Sysnand 9.2 nand to restore my emunand to 9.2 if I want t using Emunand Tool even after I have unlinked Sysnand And Emunand?
Oh, really!! And, can you please tell me how to restore my backuped data to sd card?
Yes you can use your sysNAND backup to restore your emuNAND to 9.2 with the emuNAND tool.
Is this after formatting emuNAND? If so all you have to do is copy the files back to your SD card or is this some other situation?

Yeah, it is after formatting Emunand, but when I go into SD Card after formatting there are 2 folders inside it. Also, will copy pasting the files give me back the eshop games too? Or O have to download them again through eshop?
Yes copying and pasting will give you your eShop games back.