Learn Croatian: Želiš li led i šećer? - Do you want ice and sugar?

Because they are inanimate (non-living) masculine nouns. In Croatian, when a noun is the direct object of a verb like želiš (you want), it takes the accusative case. For inanimate masculine nouns, the accusative form is exactly the same as the nominative (dictionary) form.

Where is the word for "you" in this sentence?

In Croatian, the pronoun ti (you) is usually dropped because the verb ending already tells us who is doing the action. The -š at the end of želiš specifically means "you want."

What is the purpose of the little word li?

The word li is a question particle used to turn a statement into a yes/no question. To form a question this way, you just take the verb (želiš) and put li right after it.

Could I ask this question using da li instead?

Yes! You can also say Da li želiš led i šećer? Starting with Da li is a very common way to ask yes/no questions in spoken Croatian, while putting li after the verb is slightly more standard in writing. Both mean exactly the same thing.