I ate an onion that was 3 weeks old today and it looked and smelt fine but I'm worried?

When onions aren't fit to eat, you'll know; they get moldy and mushy. Even sprouting onions can be used, as long as they are still firm (and the sprouts are good in dips and salads). When I was a kid, we kept onions, potatoes, apples, beets, and squash in a root cellar, for months. Common sense is the key; if it looks, smells, or feels 'off', it is.