In general and without context using "an" would seem a little odd. If the apple juice was in a bottle or carton then you could say "an/a apple juice" because you are referring to the container "a (bottle) of juice".
Thats not used too much in english is probably why. People a "drinks apple juice" not "an" unless maybe its a singular juice box? You wouldnt say "drinks a milk" or "drinks a water". (However you would say "drinks a soda" is its a singular container)
Because these two might not be too different in English, but they are in Korean. While 마셔요 means 'drink(s)', and refers to a general habit of drinking, 마시고 있어요 means 'is drinking' which refers to the current action