Not a huge risk, if any at all. There is one line coming from the pump, and then it splits at a Tee fitting to go to the two main drains. Each main drain sucks in an equal amount of water.
Lets say that you completely say down on top of one of them, and 100% blocked the cover. What happens in reality, is choosing the path of least resistance, it will draw all 100% of the water from the main drain that you are not blockin,and 0% form the one you are blocking, meaning that you will feal zero suction on teh one you are blocking. Same net flow, just different where it is going.
Plus, originally the main drains many years ago had an additional problem compared to just having 1 drain not 2. The suction holes were all on the top, not the top and sides. This made it easy to block off all of the holes. More modern covers have holes the top and the sides. SO if yo usit on the top, and block all of the top holes, it can still suck in water from the side holes, and thus no entrapment.
If you are worried about it, take some leaves in yoru hand, and release them a foot or so away from near the main drain. You will see that they are not being aggressively sucks in.
Leave it to my kids to figure out how to make them dangerous. They told me they couldn't get their frisbees off the bottom of the pool. What?? That's when I noticed they had used them to cover both drains. We had (another) very long talk about drowning after that.