My boat has 3 batteries: 2 trolling and 1 cranking. When I purchased the boat, the batteries were strapped down, but not in boxes. Just wondering if it's worth it to rework the battery area and put the batteries in boxes. Any advice/experience will be appreciated.

I don’t like boxes.

Just trays to strap them down is all I use I my bass boat. Now my aluminum boat I keep them in boxes because of the exposed terminals, it does not have a battery storage covered area.

wouldn't use them in the enclosed area of a bilge, they trap heat and gas while charging if the tops are on.
box with no top is no different than a tray/strap.
this is mine.

Thanks for the comments. All good points. No boxes for me when I do my fall maintence.