@eman
The holes at the bottom of the battery cover serve as drain holes designed to channel water out of the battery compartment and into the hull, where it can then drain out through the bottom plug. If you find water accumulating in the battery compartment, it's possible that water is not draining properly due to the position of the drain plug, which may be slightly higher than the bottom of the hull.
This situation could arise, especially if the boat is stored outdoors, as rainwater may collect in the hull over time. Consequently, when the boat is tilted or leaned to one side, such as when stepping down on the port side, the water can pool in the corner and reach a level where it enters the battery compartment through the holes.
While I personally store my boat indoors and rarely encounter water in the hull, I occasionally remove the bottom drain plug and tilt the front of the boat at a 35-45 degree angle to help drain any accumulated water from the hull through the plug.