if you get the modified pack of cias from that iso website related to the 3ds then it will not update mset/agb/whitelist so it wont update ds mode/dsi mode/ds profile hack
so yes with the modified pack you will need no further changes for ds games (if your flashcard works now it still will)
as for the pros of updating you can boot directly int cfw with the initial press of the power button
https://m.youtube.com/watch?feature=youtu.be&v=LcAMVMpXjzo its
the reason to update your systemnand
this is done using themehax so you need theme support ie 9.0 or 9.2 systemnand