depends on the game.
pokemon, and jet impulse for example support DLC on m3i zero.
jam with the band/daigasso band brothers DX doesn't support DLC on any flashcart due to some pretty good protections serverside.
100 classic books, and warioware DIY support it partially, because m3izero has some trouble writing data beyond the first 512KB.
don't know of any others, but as long as the save is 512 KB or lower you can be pretty sure DLC will work.