Some of the roms that have been through patchers may actually appear as clean to some tools but that is a different matter.
DS roms are usually loaded and save to the GBA slot which is something they would not otherwise do.
There exists a nice debate as well in DS roms regarding the secure area of the rom too: this area has to be decrypted to dump the rom and all roms as far as I am aware are distributed without it being encrypted once more, a few tools can do this though and this more accurately matches the data on the DS cart so in theory it is more pure.
As for advantages, in some ways there are and in some ways there are not: in the current absence of a decent cheating mechanism there are some trainers for roms which can improve the game for some people.
There are a few translations about which can obviously improve the game for some.
You can also do things like replace soundfiles: I normally stick the Japanese soundfile from Rockman into Megaman Battle Network which gets rid of the dub.
I also always drop the intro from Castlevania: it is big (dropping it fits me another game on the cart or even allows people to fit the game on their cart where they previously could not) and it is pointless to boot.
You can read more of this here:
http://www.sosuke.com/ezflash/viewtopic.php?t=457
I will damned if the above three roms do not improve some peoples playing experience and they can not be considered clean by any standard.
