Jacking up the engine to run across shallow water puts the cavitation plate in front of the propeller, actually encouraging cavitation. Lifting the engine vertically keeps the plate above the propeller and aligned with the movement of the boat. Thrust channels directly parallel to the surface of the water - the most efficient direction.
A tilted engine throws a rooster tail of water up into the air. If you throw water up, you waste energy. Plus, Newton's Third Law of Motion says that thrust upward must equal thrust downward. If you're in shallow water, you don't want your boat to be pushed down, especially at the stern. An engine tilted bow-up at a high angle to go across shallow water will raise the bow and lower the stern, making the draft of your boat deeper.
A boat equipped with a jack plate can avoid all those negative consequences of tilting the engine. By simply raising the engine up with the jack plate until it is just on the verge of cavitation, you can run and start up in far shallower depths than you ever imagined. If you want the ability to run with impunity in shallow water, meaning without tearing up either the bottom habitat or your equipment, one way or another you need to raise the skeg and propeller on your boat higher, and the jack plate represents the best possible means to accomplish that.
One other thing many knowledgeable boaters ask: "Why doesn't lifting the prop up like that raise it right out of the water?" For the same reason that high-speed performance boats use surface-piercing props. Once the water under the boat passes the trailing edge of the transom, it angles upward. So even when the prop is higher than the bottom of the boat, it sits far enough back to work in solid water.
Better Gas Mileage Too
A jack plate also increases fuel efficiency. Simple logic dictates that when you can channel-thrust directly parallel to the surface of the water rather than up or down in comparison, you waste less energy. Additionally, the lower drive unit, prop and skeg all create drag in the water. With a jack plate, you can raise the engine higher in the water column, thereby decreasing drag. Certainly, you may need to lower it farther into the water in rough-water conditions or in turns. But calm conditions will allow you to run with the engine higher and burn less fuel.