Depending on the engine, it's fairly easily possible to modify the electronics so that an additional component is needed to start the engine. That component of course you carry with you. Because it's a non-standard mod no-one has a clue what's wrong and it defeats them. I've never done it with a boat engine, but I have to car and motorcycle engines with apparently great success. Easier with 4-strokes than two, and doesn't work at all with diesel.
Of course, that doesn't stop the theft of prop or lower unit. We had a spate of those thefts a while back, but I haven't heard of any recently.