It's those key words, every language has in some form. That everyone would find some difficulty to be without. In fact, these two words are more likely to be learned by those who don't speak English. Just as many English speakers are more likely to learn the yes/no equivalents of another language before traveling abroad.
Although, there are plenty of substitutes to 'yes/no.' But, since the words already exist, many people would probably prefer typing yes/no over affirmative/negative (among other variances). But not always. I often hear more variety in yes/no varieties spoken then I do see written.
So, it's here to stay. No need to change what works so well.