Why wouldn't "who wants coffee" be "kdo chdete kavu"? You're asking 'which one of you (plural) wants coffee?" You plural is, vy chcete. Isn't it?
Because that is the most common expression for that in Czech. "Kdo chcete kávu?" is not impossible, at leas colloquially, but is more like Who of you wants a coffee? (i.e., you are addressing those people directly)
Surely "who wants a coffee?" is also correct as a translation. Kavu is singular, right?
Even if it were impossible in US English, it is possible in other varieties and therefore accepted https://en.oxforddictionaries.com/grammar/countable-nouns