If you wanna play the most recent games or use online you typically got to stay up to date with the latest FW. If you're using it for homebrew it's a good "rule of thumb" to keep the sysNAND as low as possible for possible future exploit options. emuNAND can be updated to the latest FW (as long as atmosphere is also updated) using daybreak if it's dirty or normally I'd it's a clean NAND (no illegitimate titles, saves, etc) with the only drawback being if you're game card slot and current switch firmware do not match then the game card slot won't work (unless there's a workaround Im not aware of)
That said if it's an RCM exploitable switch you really don't NEED to stay on a low firmware as the exploit is at the hardware level and can't be patched by updates. So you can keep both updated on the same firmware. I think it's 4.1 and under that have a software exploit at the moment, all others are stuck using our jiggys and a PC, or a modchip