Im personally not too knowledgable with this but over at GBA Temp theres news of a loader that runs from an SD Card, I don't condone piracy but its an interesting release none the less:

Thanks to the work of ahezard, Gericom, Apache, Robz8, _catcatcat, and shutterbug2000, we can now load NDS games from the SD card, without any flashcard/SLOT-1 card.

As promised, a release is here, on Christmas/Christmas Eve.

Don't expect high compatibility or save support yet, but do expect many, many updates.

shutterbug2000 said:
A fair warning and note to all: If you don't wish to save, keep ALL cards out of SLOT-1. THE SAVES WILL BE OVERWRITTEN IF THE SAVE CHIP MATCHES.

For example, running MKDS with an AC:WW game in SLOT-1 will overwrite AC:WW's save, since the chip is the same.

However, if you wish to save like this, TWLSaveTool can tell you the chip type. Just backup the old save first.
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Have fun!

Some games that work well with this version:

Warioware: Touched
Mario Kart DS (if you have a physical MKDS card for saving)
GoldenEye: Rogue Agent
Space Invaders DS
MegaMan ZX
Yoshi Touch & Go

Release Page link -->