This is a very situational question. It really depends on a few factors. The biggest is whether you are staying in the property during the process of the short sale.
The question you need to ask yourself is...what does the HOA fee provide and why would I need whatever that is.
Your concern is really based on two scenarios: Do I need it because I need it to stay in the property, or do I need it to keep me from some future liability.
My advice to most people is if you are looking at a short sale, it would be wise to get some advice from a bankruptcy lawyer. The concern here is that even if you do a short sale, you could still be liable for a deficiency on the HOA. Many lenders are not giving people full forgiveness of debts. I'm predicting a lot of people needing to file bankruptcy over the next 6-8 years because of debts they thought were resolved in a short sale that come back to haunt them.