If you have, or suspect you have, water in a deck core, the way to tell is to simply drill a couple of small holes in the underside and see if water runs out. The best way to repair deck cores is from the underside when that is possible. Making repairs is easy, but putting back together everything that has had to be torn out is where the real work comes in. The problem with repairing from the exterior is that it is extremely difficult to accomplish a finish repair that doesn't look like its been repaired, and its not a job for an amateur. If you can't make the repair from the underside, you should not try an exterior repair yourself unless you are highly skilled in this sort of thing.
Few people are.
If you can't get access from the underside, then you have a major and costly problem on your hands. A pervasive problem, window frame leaks almost invariably occur because the structure in which the frame is mounted is weak. That usually means either the deck below or the house top above it is distorting and causing the caulking seal to break open. One possible method of repair is to remove the frames and to reset them using bolts instead of screws. Here's a possible solution that will require several days to accomplish.