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?)
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?
The sentence "What if they were made from cow droppings?" is in the past tense. The verb "were made" is a past tense construction.
To determine the tense of a sentence, you can look for verb forms that indicate a specific time frame. In this case, the verb "were made" indicates an action in the past. The word "if" is typically used to express hypothetical situations, but it does not affect the tense of the sentence.