Actually, I have emunand installed on the hidden partition and I have plenty of games installed to 'system storage' within the emunand. I do it to avoid having 'wasted' space on my sd card.
When you choose the hidden partition option SXOS repartitions your card. There willl be a roughly 32GB partition that you wont be able to access normally, and it will show as allocated space. Whenever you choose to install something to 'system storage' within the emunand, then it gets stored within that 32Gb partition. If you never use the 'system storage'option on your emunand, then you literally will have 32Gb of wasted space on your sd card. It wont harm you, but its a waste... literally. Everything you choose to install 'to sd card' goes in the Emutendo folder. So in the end everything from emunand is within the sd card, leaving no traces on the actual sysnand.