@ofy90
Yes, it has been explained multiple times, but np, I’ve time right now. 
Presets-4.1 contains presets made when koko-aio was at version 4.1, which is pre NG.
They share a distinctive mask, the only one possible at the time; the look of those presets is meant to be frozen, apart from minor tweaks or from time to time.
Presets-ng contains presets made after koko-aio ng version was released.
ng release carried a complete rewrite of the mask code allowing it do be far more flexible and feature rich, while mantaining the ability to replicate the old code.
> Read more here <
New presets will appear there.
Presets:Handhelds-ng contains presets to emulate handhelds possible after ng version was released.
Nope, there are no such thing; the main koko-aio folder does not contain any preset, apart from the koko-io-ng.slangp which is meant to be the parent of all the presets, but is not meant to be used.
However is true that there are duplicates names; the folder:
Presets_HiresGames_Fast contains a copy of the 3 afromentioned folders (4.1,ng and handhelds) which are intended to be more performant with cores that have an high output resolution (dreamcast, ps2…) > Read more here <
The advice is to just pick the one you like, easy.