[Spring44]

Bearing in mind that any trunk/hatch is prone to being overrun with water in a hard rain, here are a few things to consider.

1)Is the water running off of the roof and down the body channel then over/under the hatch seal rubber?

2) Or, is it running off of the side of the hatch glass when it is raised?

If it is 1), then check to see if the rubber seal is tightly attached to the body along the top and side of the seal.

If it is 2), Then your spoiler drain holes may be plugged causing the spoiler to collect excess water and that water is being suddenly dumped off of the side when the hatch raises up. Clear the spoiler drain holes.

As to the hatch not latching, if you have new struts they may be pushing the hatch backwards away from the front hinge when it is opened. Hatch glass separation is fairly common on these old cars and will cause a misalignment of the latch and the latch pins, making the hatch hard to latch.
Disconnect the struts, then gently push forward on the hatch/spoiler to realign the latch pins with the latches. The hatch pins ought to latch after you do this.
HTH