Warmboot is confirmed up to 4.1 however there is no currently estimated window on when it will be available. There is a new Switch revision supposedly works named Mariko which is likely when this warmboot will see the light of day but currently there is no evidence of that either. The benefit of this warmboot is that it doesn't involve a jig and USB cable so it involves less hardware in order to load CFW/hacks. If you're holding out for warmboot but want to update your firmware, I highly recommend you check out the homebrew ChoiDujourNX which can update your firmware without burning fuses. Burnt fuses are what prevents downgrading in the first place so if you do not burn them, logically speaking, it allows you to downgrade to the firmware you were originally on.
Not sure what the compatibility of custom themes is with respect to firmware except that they do not work on firmware 6.0 so if you want to use them, at the very least, you would do well not to update to that firmware. If you must update, 5.1 is the best firmware for CFW currently which you can do so with the aforementioned ChoiDujourNX.
You can restore your clean 4.1 NAND, then update to any firmware you want, and then you can make your EmuNAND partition. However, you cannot restore the clean NAND and avoid having to reinstall all of your backups; its one or the other since the clean NAND doesn't contain any of your backups (because its clean).