The verb in sentence 2 is in the subjunctive mood.
http://www.englishclub.com/grammar/verbs-subjunctive.htm
So even though it seems to be in the past tense, it isn't. The "what if" makes it something imagined, not real. Therefore, it's in the subjunctive.
A problem I see in sentence 2 that you didn't ask about is the pronoun "they." What is its antecedent?
1. Do you like vanilla-flavored ice cream? 2. What if they were made from cow droppings?
(What is the tense of Sentence 2? Is #2 in the past tense or the present tense?)
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