If you have water coming in, you want to address it. Otherwise, the core gets soaked, leading to delamination. A couple possibilities; it may be coming in at the bases of the pulpit, or other through bolts, or possibly at the rub rail. Given the stress cracks you showed, I would be inclined to rebed the rail. In fact, since it's a recent purchase, I'd probably set about with a plan to rebed everything on the deck eventually, from stem to stern, unless you are certain they've been done recently. It's not urgent to do so, but this is a maintenance issue.