There's probably a good chance that you're saving your roms/patched roms within one of the folders in the install path. The way Windows categorizes the size of an install is not by the size of the base install, but by the size of the folder and everything in it that it was installed into.
Example: You install the supercard program to C:\Program Files\Supercard\
Let's just say it takes about 10 megs of space. But then you patch all of your .nds roms, and they are output into the C:\Program Files\Supercard\patched\ folder. Let's say your total amount of roms you patched added up to 570 megs. Windows then looks at the C:\Program Files\Supercard\ folder and sees that its total size is 580 megs (because of the sub-folder). That would explain the reason why Windows thinks it's so large in the Add/Remove Programs list.
That may not be your exact situation, but I think it's close/a pretty good guess.