DS cards come in 8MB 16MB 32MB 65MB and 128MB, when a game is written to one, it has "Filler" data to take up the space between the games actual size and ds cart. Trimming the rom removes the "filler". The only negative it has is that it breaks download play, other than that, nothing.
I made a trimmer that detects wifi enabled games and won't break them. It also supports zips and batch processing. http://techsuki.net/nintendo-ds-rom-trimmer/
