I think it depends on the situation.
Say for example you are in class with many other students. The teacher wants to make sure everyone understands and so she says, "if you have a question raise your hands".
Since she is talking to many people, even if she wants everyone to raise only one hand if they have a question, she uses the plural "hands". This is not grammatically correct however.
Since she is talking to "everyone" as individuals and not as a group to see which individuals understand, she should say "raise your hand if you don't understand"
If someone wants you to raise both hands, she would say, "raise both hands"