Allays can pick up a whole item stack at once but when they throw it down near noteblock they throw the items 1 at a time. This is inconsistent with how they pick up items (they dont pick up items one at a time). This is also problematic with hoppers as hoppers have cooldown after picking up the first item which makes other items the allay throws end up in other places with their momentum. 
See image of items not going into first hopper but flying into nearby hopper.