no, items installed install a ticket to the nand you are currently running, so if you install anything in any of the nand's sysnand/emunand1/emunand2, it will only work in that particular nandand for installed things? like eshop games or program like savedata? i can launch my eshop games on NTR CFW if is linked with 9.5 emunand?
also the NTR CFW does not run unsigned cia files
so just to make sure everyone is clear, this will not allow people to run cia files in anything other than the normal leaked cfw, unless you own a MT/gateway card