There are various reasons, especially based on the Ayurvedic medicine… which teaches us that the onion CAN be consumed, BUT… as a medicine, because it has countless qualities which are very advisable for ones health, but not as food…

The onion is catalogued as one of the nutriments that correspond the quality of ignorance, or “tama guna”… because it grows and develops in the dark, that is under the surface… it does not absorb the solar energy and the fresh air that convert it into an nourishment of very scarce “prana” or vital energy… Apart from that, the onion is considered to be an aphrodisiac that agitates the sexual instinct, which is just the opposite to what the Vaishnava wishes to arose…
A devotee of Krishna is aimed to control the senses, and especially the desire for sexual enjoyment…