Sorry, but it's just stupid anyway for a boat to be designed so the ladder can be hit by the props. No excuse for that whatsoever. I would contact Sea Ray and ask for a new ladder, since it was because of their flawed design that the problem happened in the first place.
Other than that, yes make sure that you don't run with your outdrives too far up, although many many many times I have run the boat with the outdrives about 1/3 up at idle speed in shallow water, and of course I've never had any problems. I've also forgot the ladder in the down position a few times, but in our boat it's impossible for the outdrives to hit it. The extended swim platform is extended enough that they never project beyond the platform, regardless of position, and the deployed ladder sits *beyond* the platform and cannot swing back underneath it.
Many here think things like this would never happen to them, and yes, if you are careful and operate the boat correctly, things won't go wrong. However, we ALL forget something and screw something up at some point, and boat builders should help us out by not doing stupid things like putting the ladder in the path of the props if you forget to retrieve it and also forget to trim back down far enough. It can't be THAT hard for them to figure this out.
Oh, and also make sure you have a pro take a look at your props. I bet they have some damage, and even minor damage can affect performance.