That Hamilton Woman 1941 AKA Lady Hamilton

Very impressive miniature effects in this film supervised by Lawrence Butler. Must have the most square rigged model ships in a studio tank ever. The pyrotechnics are also spectacular and the sheer volume of smoke from all the miniature cannon fire is staggering. The models also take quite a battering with quite a number on fire and a few exploding sending wood splinters flying.

I suspect the model ships were built in the "British" fashion with open bottoms and riding on trolleys that ran on rails on the tank floor (see this page Model Control). The distant ships are just flat painted cutouts positioned at the rear of the tank on the ground in front of the sky backing. 

Many of the live action battle scenes use miniature shots as rear projected backgrounds.

The Victory miniature used in the film is preserved and on display at the Historic Dockyard, Chatham. The model is 7.6m (25feet)  long and 6m high. I am guessing that this is probably 1/16 scale which means that on the model 3/4 of an inch equals one foot of the full size ship. You can see in the photos below that the model has a flat bottom and not a complete hull. This would not have been apparent when in the studio tank.

Wake of the Red Witch 1948

This being a Republic Production means that the miniature effects were handled by the Lydecker brothers Howard and Theodore. The special effects credits are sub-headed under-water sequences although there are some miniature surface shots of model ships as well. 

The bulk of the work is indeed in an underwater setting with a miniature shipwreck teetering on the edge of a precipice which eventually slides over the edge. There is also a marionetted diver figure with subtly moving arms and legs along with the emission of a stream of bubbles.