Not only is it beyond obvious that WhatsApp stores that data, it's actually better than for example Telegram, which also stores all that data, but in addition to that can MITM all your "non-secret" (read: probably all, nobody uses that feature) messages if they choose to.
It's honestly the best we can ever hope for in a free but commercial product. Everything with better privacy would either have to run almost server free or cost money. Both of which would probably kill mainstream adoption for different reasons.
Not to mention that even if everyone was willing to pay $1 per month for a messaging service, now people are instantly identified with a bank account. And even if you allowed bitcoin, since 99.9% of people would just use your bank account, not using one would instantly put a spotlight on you. And who sends messages to whom is still going through their servers. To actually get significantly better privacy, you'd have to essentially use the Tor network or something.