Learn French: Je voudrais des truffes, s'il vous plaît. - I would like some truffles, please.

You would say J'en voudrais quelques-unes. Because truffes is feminine, you use the feminine pronoun quelques-unes (a few). You also must add the pronoun en before the verb to replace the idea of "of them" (of the truffles).

Why do we use voudrais here instead of veux?

Voudrais is the conditional form of vouloir (to want). Using je voudrais (I would like) instead of je veux (I want) is the standard, polite way to make a request in French, especially when ordering in a shop or restaurant.

Why is it des truffes and not les truffes?

If you said les truffes, it would mean "the truffles," implying a specific batch (like the ones you are pointing at) or truffles in general. Using the plural indefinite article des means you are asking for an unspecified quantity, which translates perfectly to "some truffles."

Does truffes refer to the rare mushroom or the chocolate?

It depends entirely on the context! Just like in English, une truffe can be the expensive underground fungus or the rich chocolate treat named after it. Since both are countable and feminine, the grammar of the sentence stays exactly the same either way.