Granted, the saves are binary blobs but once you find the value you want you can find an entire struct of data along side it. There are tools like imHex which help the process and help you define the structure of the save file. It's become a common project of mine to save hack and then build a save editor when I'm confident my changes work.
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.