Some mollies will eat their fry, so that would be my suspicion if they're disappearing. Other deaths may be caused by water quality or lack of fry-sized food. In my tanks, I change 20-50% of the water every week.
When feeding fry, I use special livebearer fry food, crushed tropical flake, and occasionally crushed dried bloodworms as a treat. Live plants usually have plenty of microbes for the fry to feed on in the first few days. I use a pistol and mortar to grind the flake or bloodworms into a powder. Adults have no problem eating the powdered food.
Mollies need lots of room to roam and have a tentancy to freak out in nursing "traps". I prefer to provide fry with plenty of cover and keep them in the same tank as the mother, or even in the same tank as a breeding trio (two females and a male). You loose some fry to the adults, but livebearers produce plenty over time.
In your case, some top cover in your display tank should be ample to give you a few surviving fry every month. The placo is likely to be efficient in finding any fry that heads for cover in the bottom of the tank.
Young mollies may only drop a dozen or so fry every month. By the time they're a year old, they should be dropping about 25-50 fry a month. They can drop more than 100/month when they get to about 3" or so.
An important aspect of breeding livebearers is having a plan for all the fry. Be careful to keep the maturing males away from their sisters, or you'll quickly be flooded with more fry than you can raise. A molly will have fry for up to six months after being separated from males. I sell my fry to the LFS. I only get 1/3 of the retail price as store credit, but it pays for fish and bird food plus other supplies. Most chain stores won't buy them, but will take them if you want to give them away.