Ebay have been instructed to pass information, including NI number, to HMRC when sellers pass certain thresholds.
Ebay don't know what individual sellers do regarding their tax, and the only way for Ebay to get your NI number is to ask for it.
"There are two ways to be fooled. One is to believe what isn't true; the other is to refuse to believe what is true.”
Søren Kierkegaard, Danish philosopher (1813 - 1855)