Anything you can buy today will use an external memory card for long-term storage. The days of reflashing the cart just to change the current game are long past. Even if you have an old cart, typically you can add more *.gba files to the end of the cart as long as you don't exceed the cart's overall capacity.
Unless you have a Flash2Advance cartridge and are reflashing a new Pogoshell image every few days, I wouldn't worry about it at all.
EDIT: Re-reading the original post, don't forget that every flash cart has its own internal bootloader that lets you choose which *.gba file to launch.