These days it's far easier to read/edit the memory of running programs than the serialized data saved to disk in save files.
Asking because I don’t actually know, I’m just recalling a lot of my early ROM hacking, and indeed discoveries in ROMs, by manipulating memory and savestate rather than the ROM itself.
In a general sense, I suspect the latter is more popular because it's not illegal to modify/distribute save state data; ROMs certainly can be.
Obviously, if you want all 151 Pokemon captured, you would do that through a save state. But if you want increased chances of capturing Pidgey, it would certainly be easier to distribute a ROM (or delte, in this case) with those new ratios baked in.
To hack a ROM you need to know how to decompress the data, and then recompress your changes. A given game might use multiple compression formats.