Water electrolysis is around 60-80 percent efficient. Hydrogen fuel cells are around 40-60 percent efficient. Plus you spend additional energy to either compress or cool the hydrogen in order to be able to store it.
Electricity storage in a lithium-ion battery is on the order of 98% efficient, and electric motors are around 90% efficient (if you take into account the whole drivetrain).
Yes, hydrogen and ammonia handling efficiency will mostly go up, unless extra-cheap (to buy) electrolysers come out with unfortunately lower efficiency.
What always matters most is cost. Inefficiency will get cheaper and cheaper as generation cost falls. Switching from gold & platinum catalyzing electrolysers to something not dependent on those and less efficient is still a win if you get a lot more electrolysers for your money.
Electricity storage in a lithium-ion battery is on the order of 98% efficient, and electric motors are around 90% efficient (if you take into account the whole drivetrain).