Yes, exactly. What happened was that the ship fired salute to the king (ironically enough) just before it sank. So when the boat leaned over due to the wind gusts, the canon hatches were open and the lower deck flooded quickly. Ultimately, Vasa had design flaws, so this was inevitable. The dutch shipbuilders were the best, but they had never designed such a high ship with dual cannon decks before so this was unexplored territory.
The guides and info brochures told about four deaths. One crewman was stuck after a cannon rolled over his leg, and he drowned. They actually found him like that, quite well preserved
So that's how they know. Two captains "went down with the ship" trying to straighten her up until the end. One nobleman fell as the ladder to the top deck was snapped in half, fell unconscious and drowned....
