Translation:Two glasses of orange juice, please.
Because that's the English idiom. Two glasses of orange juice, a glass of milk, a cup of tea, a glass of wine. If you asked an English speaker for two glasses with orange juice they'd think you meant the orange juice separate rather than in the glasses. Preposition use varies from language to language. The only way you would use 'with' here is 'two glasses with orange juice in' which is both unwieldy and not used by natives.
When talking about food and the ingredient is the main or only component you say
Dish DI ingredient
Soup of tomato
zuppa di pomodoro
but we would then have succo di arancia so because orange in Italian starts with a vowel you drop the i to get succo d'arancia - juice of orange.
Actually, saying it this way could imply that you are specifically asking for two glasses that are for orange juice only (kind of like asking for a wine glass or another glass designed for a specific beverage). You are not necessarily asking for two glasses containing orange juice.