I feed amounts of micro and banana worms that would make some breeders angry at me. I'm serious. For the first month of their life, they get microworms 90% of the time... And they turn out just fine. I've had one case of missing ventral fins, and that was on a fish that didn't grow properly.
I find the "nutritional deficiency" theory highly unlikely, because it shouldn't take any different nutritions to grow the ventral fins than any other fin. I just find it extremely strange that a nutritional deficiency would cause issues with the ventral fins and nothing else.
The bacteria theory makes some sense, as fry spend a lot of time at the bottom, where the worms sink to. The main issue I have with this is that it should affect the anal fin too, but I suppose the fact that anal fins develop much earlier than ventrals, which some in later, could explain this.
Either way, I never experience any issue, probably largely because I clean the bottom fairly often and have snails to do it for me in the meantime. I can sent you to some discussions we've had on the topic, if you want.