But, in good(?) news, I may have figured out WHY Puddles disappear from the docks.... unfortunately, though, it's because they're actively committing Puddlecide:
o^o
And no, this was not a one-off thing. I've tested it multiple times trying to get a gif, and is seems that as long as the puddle is near the edge of the pond, they decide they want to go all Little Mermaid on me.
Then again, I have 4 ponds full of puddles just off-screen with toys in each one. Maybe they're being drawn to the quacky goodness that are the rubber duckies?
Edit: It's DEFINETLY the ducks. I moved one duck over to the waterfall pond to draw the puddles away from the edge, and the puddles in the pond I took it from IMMEDIATELY started jumping over (and sometimes succeeding!) to get in the pond next to them that had a duck.
They're being seduced by quacking sirens of death.