yes
I managed to get linked emunand and sysnand to use different theme (and even different internet profile), but I don't quite remember the steps
I think it involved something like setup theme in sysnand and emunand, and afterwards restore nand backup of either (I did both sysnand and emunand though)
in the SD card, there is only 1 directory with random number, so that means it still linked right? but they now have different themes now
these steps not guaranteed to work on everyone though, might be just a glitch that happened on my 3DS