I don't personally face this issue because the only real pest animal around my area currently are rats and the cats have kept them in check.
What are the main pest threats your looking at locally? You might be able to get away with a closed container set up for composting.
1. I use duck poop all the time with no special accommodations. If it's from the pen it goes into a compost pile. If it's from the kiddie pool it's drained directly into one of the gardens.
2. I lock mine up at night with no food or water. They aren't always content but they are safe. Which...
Actually yes you can and it defiantly helps keep the water cleaner. I know there's at least one thread about it on here but for the life of me can't remember the name of it.
Yes pond pumps are useless with domestics. I ended up buying a sump pump and it is truly one of the best things I have ever bought. It's come in handy for so many things besides just the ducks.