.3ds are good for archival dumps that projects like no-intro catalogue (although they are cataloging clean CIA files too), and for sky3ds users clean .3ds dumps are essential, gateway and cfw on the other hand can use tools to swap between .3ds and .cia and still use the resulting file
But threads like this (there has been a few over the past few days) are like saying "why does dialup exist when we have broadband". ........obviously things change, progression happens and things become out dated, that doesn't mean they should all just be wiped from existence because something better in 99% of scenarios came along, if you don't use it, don't use it, if someone refuses to move on and would prefer to stick to their old dialup leave them to it