Translation:Do you speak Italian, French, Spanish or German?
Does Esperanto make any intonational distinguishing between 'do you speak A or B (ie. do you speak one of these, or something else?)' and 'do you speak A or B (ie. which of these do you speak?)'
In English I guess they'd be set apart by stress, so in the first sentence 'speak' would be the primary focus, whereas in the second, 'A' would be more prominent, but I'm curious as to whether Esperanto has any similar features
That's a logical conclusion. But for some reason also multiple-choice question in Esperanto are used with ĉu, e.g.: "Ĉu vi volas trinki teon aŭ kafon?", or "Ĉu via infano estos knabo aŭ knabino?" - it can be understood as a truncation of "Ĉu vi volas trinki teon aŭ ĉu vi volas trinki kafon?". So indeed you can answer that first question with "Teon!", "Kafon!", or simply with "Jes!" ;)
Regarding the ambiguity resulting from the possible translations "Do you speak [ever]..." versus "Are you speaking [now]...":
Perhaps it would be more understandable to ask "Can you speak...", "Ĉu vi povas paroli..."; Or "Are you able to speak...", "Ĉu vi kapablas paroli..."