Time was I would trim SDAT files with a hex editor (no attention to the header or anything) and the rom would still work although that is not quite the same.
Anyhow yes you can just remember to double up on anything that you remove similar to how you might for a basic audio tweak hack and redo the pointers (header, FAT section, symb, info and the like) as you probably expect to. Everything else should be unaffected/self contained in their sub files.
I have to ask though- are you really that close to the DS rom size limit- 32 bit reads make for a 512 meg game give or take the header.