Oh ok sorry i didn't realize you had a PAL 3DS. I have a US 3DS so i don't have update nag
But my guess is that you can safely system format 4.x sysnand without breaking eshop access on 9.4 emunand. When you do system format earlier, it was from 4.5+ sysnand, which knows about NNID. Part of that system format tells Nintendo's servers that your NNID is unlinked and doesn't belong to any 3DS... that's why you can't use eshop from emunand. Cuz nintendo's servers know the NNID is gone
But in 4.x system, there is no NNID at all, so I don't think formating it will affect your eshop access
But don't quote me on this, I'm just guessing here