Depends on the flashcart, you will not have lag,s the unit will fail to start as it will corrupt.

When you put on the .nds files, as each starts it creates a .sav file, depending on the card also an option file, cheats? you need to leave room for all.

As a guide I use 1mb per game, most sav files are 512kb although some are 1mb. But 1mb per game should be fine

 

It could be the SD card - it will not be the space but the speed of the memory card - class 6 is the best, alternatively you could try formatting your existing card (after backing it up) with Panasonics SD Formatter (free - use google to find) it formats SD cards correctly, not like windows which does not this can speed up the access time