If you're on 4.x or lower and want to be able to use PegaScape to boot CFW without using a jig or payload dongle, don't update.
If you're higher than 4.x, there's no real reason not to update. Be aware that if you're on 8.x your game cartridge slot will be updated. This will cause Atmosphere to crash if your emuMMC is on an older firmware and a cartridge is in the slot. But don't worry, if you don't use cartridges in emuMMC, just leave it ejected and everything else works fine.