The app stores operate there as distributors. Just because my product is distributed somewhere by a third party doesn't necessarily mean I operate there.
If an art dealer sells a painting to someone in brazil, does it mean the original artist operates in Brazil?
I think the difference is that you /knowingly/ (to an extent) sell your app to Brazil. If you sell your art depicting, say, women in power to Saudia Arabia to someone here and they move to Saudia Arabia and sell it, it's not your fault. But if you told him it's ok to sell that painting in Saudia Arabia, I would assume you can be held liable.
(Not that I agree with that, but that's what it looks like)
In the artist/dealer scenario, only the latter is actually under the legal jurisdiction of Saudi Arabia and could be legally compelled to follow a court order. They can choose to hold anyone liable but their legal and practical ability to compel an entity to comply doesn't extend beyond their state unless they have an agreement with another state.
Apple has a corporate office in Brazil (google too) and they're the ones who distribute and approve the application for sale there. They're legally required (I assume) to respond to legal notice they're served with. WhatsApp is not legally required to do so, and others have pointed out that it might not even be legally feasible for them to do so.
Of course this situation is more complex because obviously Apple doesn't have the data and I doubt Brazil wants to get into a legal battle with Apple. And although Brazil doesn't have the ability to force WhatsApp to comply with anything, they do have the leverage of being able to shut down their service. Should make for an interesting story to follow.
At the very minimum, if they had served Apple/Google instead, they would have had a legal requirement to actually respond. I don't know much about the actual case so these are mostly assumptions.