When Alpha Strike chooses multiple enemy units, can I choose to deal 0 damage to one of those units?

No. Each unit you target with Alpha Strike must receive at least 1 damage.

Per Rule 355.14.g, "Valid damage is a positive integer amount, greater than or equal to 1 damage." Since Alpha Strike splits damage and each chosen unit is a target, you cannot assign 0 to one of them — that wouldn't be valid damage. If you target 3 units, you must have at least 3 total damage to split (1 to each).