Because lemons are freaking awesome
But seriously, I imagine it went like this: Bono wrote Lemon based on his mother's dress, then when PopMart came along, they drew the connection because:
1. lemons are freaking awesome
2. the
song Lemon is freaking awesome
3. the tour theme was of a supermarket and lemons are sold at supermarkets
4. the whole stage setup was so over the top, that once they decided they wanted a giant mirrorball
something on the stage, a lemon seemed like an obvious choice for a shape for it, to fit the recurring theme
5. once they'd decided on the mirrorball lemon, everything thereafter (such as the lemons in the Last Night on Earth video) fit perfectly
Also, don't forget, they also had an olive
....and I put too much thought into that.