Did they discover how their wallets were hacked?
It seems to be unclear, but in the thread on the subject they say this:
The hacked activities were made by their team who is behind on this major issue? (because I'm thinking this way)
We can only speculate, but from what i have read about the hack, many people are suspecting this to be what happened, it was probably an inside job, maybe someone in their team added something malicious to their code, but until Atomic Wallet tells us what happened, we can only speculate, that's why closed source wallets aren't good.
The point is to avoid closed source wallets like the plague.
Its a warning as you have pointed out, dont trust Hot wallets, hardware wallets are the best places to store your Bitcoin and crypto.
Yes, but while you're at it, you'd better choose an open source one.