A good picture for this word is a number being set back to zero. Something had force or value a moment ago, and then a stroke of a pen, or a change somewhere else, leaves it at nothing. The word does not say the thing disappeared; the paper is still on the desk and the money is still in the bank. What has gone is the counting: it no longer adds up to anything.
From the word’s history
The word is null plus -ify, that is, to make something null — to make it zero. The zero in the root is why the word is so total: nullify is not to weaken something, it is to leave it counting for nothing.
這個字是 null 加上 -ify，也就是「使它變成 null」，變成零。字根裡那個「零」，正好解釋了它為什麼那麼徹底：nullify 不是把東西削弱，而是讓它一點都不算數。
Wiktionary etymology in this packet (source_ref kaikki:3f6f69a190036ae4:39660147:28259): From null + -ify.
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