Many wild bananas have flowers that grow downwards, and have seeds (source, I've worked in two botanical gardens and lived next to one in Kenya, and have seen thousands of banana plants and grown many in my own garden).
The lack of seeds in the major crop bananas is due to selective breeding for seedlessness. Usually what happens with seedlessness is some part of the seed development or maturation molecular pathways are broken by a mutation, and selective breeding is used to fix that trait in the population (source, former seed biologist).
So the seedless banana plants are not generally weaker or stronger, just that they have a very specific mutation that prevents normal seeds appearing.