Does a question mark on a box stand for X?
It would depend on the context.
For example when voting in a British General Election you are supposed to put an X next to your chosen candidate. Any mark which the counter/teller feels indicates a vote is acceptable but a question mark indicates there is not a clear choice.
When filling out forms the instructions will usually make it clear what you have to put in the box of your chosen response. This is usually a tick or X. It is unlikely to be a Question Mark unless it clearly states that is acceptable, for example it may represent Don't Know.
Therefore I would argue that normally it does not mean an X.