Even in presence of CFW, I still like the option of flash cartridges. The third party device allows for an additional slot for storage. For devices that lack internal storage (NDS/DSLite), it's obligatory. While you could do without for the 3DS given the internal SD, you can cut costs of SD storage by buying two smaller capacity cards rather than one large capacity at a potentially better price.
Furthermore, you increase the overall ceiling FOR capacity. if 128 GB is truly the limit, a flash cart and internal storage in this limit can be up to as high as 256GB
And to respect to flash carts vs CFW. Both use bypasses and manipulation, but it seems nicer to be able to use psuedo hardware to get something done rather than use software to emulate pseudo hardware to get something done. Less roundabout.