The trim rom option on SC cuts the ends of DS roms that are filled with blank data, as the dumps are made from fixed sized rom chips..8mb ..16 mb and so. So a 8MB rom might only have 1MB of game data(example..game and watch rom), thus the trim rom option saves 7MB. On a lot of roms this can add up to a lot of space.
I always put the option on for SC with every DS rom, I have never had one not work, and as said the EZ4 which I also have doesn't even give you the choice, it just auto chops them (good idea..I say why not).
Both the SC client and EZ4 client reads zipped files, as already said, the client upacks them before processing in you're PC's temp folder.
But the SC can store zipped up GBA roms (not DS) on the mem card (you have to use patcher 2.53 or less), this can also save loads of space but the roms can take twice as long to load up. I have most of my GBA roms on SC in their zipped format, as I don't mind waiting 10 to 20 seconds for them to load... why not use the free space.