This is my exact experience with DBeaver. Absolutely cannot stop all the frustrating popups. Finally got fed up and started using vim+dadbod and while the experience is a bit less batteries-included, I was mostly just using DBeaver to run raw SQL anyway, and have been on vim for over a decade so that's an option for me. Now my SQL queries live in per-project versioned files instead of some eclipse project folder somewhere and I can edit them with all the power of vim which speeds up my workflows.

But nobody's going to do this without being a huge vim nerd, so I recognize it's not a general alternative.