Question: I read that 'stand for' means 'To represent; symbolize,' and now I'm wondering whether it can be used in reference to an acronym.

For example, is it proper English the following question ...

'Can you tell me what D.S.J. stands for?'

... in order to ask what 'D', 'S' and 'J' mean?

I'm asking because it is unclear to me what the difference between 'to mean' and 'to represent' (or 'to symbolize') is. 

To me, a more natural way to ask the above question would be ...

'Can you tell me what D.S.J. means?'

'to mean' seems to me more proper than 'to stand for' which I would use almost only if an abstract concept, rather than an acronym, is involved.

Answer: 
Yes, IBM stands for International business machines .
Yes. The sentence is valid and means as you described it.