As for the livewell, yes it is normal for it to be wide open hole. Stay out of the seaweed!
As for the fishbox, it is a combination of things. First and foremost the drain that allows it to drain into the bilge area must be plugged. I personally keep a little weedeater string in the boat for clearing out clogs. If the drain is open and flowing properly you shouldnt have an issue.
However, I am also guessing your splash wells are full of water. This adds to weight in the rear and helps allow water to re-enter the boat through the scuppers. Triumph is working on developing a fix for this issue (water in the splash wells).
As an added safety factor, should you loose your bilge pump, you can get boat plugs to fit cockpit drain holes. This will stop the water from entering the cockpit and filling the fishboxes.
Hope this helps
PD