Are these phrases exchangable when talking about math? refer to, denote, represent, stand for?

They are not all interchangeable in mathematics, although in some other contexts they might be.

"Denotes" and "represents" both mean that the letter X is substituting for a variable. These are correct in a mathematical context and I would imagine are interchangeable; however if you are looking for one definitive term to use it would be better to ask on a mathematical site rather than a grammar site.

"Refers to" would mean that X is a marker for a reference - I don't believe that is appropriate in this context.

"Stands for" is not normally used in mathematics either, as it can mean that the letter is the first initial of something. For example, the 'e' in 'e-mail' stands for 'electronic'.