The reaction may be at equilibrium, but the equilibrium may lie well toward the products side. You may be thinking of equilibrium in more mathematical terms, such as 1 = 1. That is not necessairly the case when talking about chemistry, though, when the equilibrium may lie toward one side or the other. If HA is a stronger acid than HB, then the equilibrium should lie to the right, as you have stated. However, there will always be a small percentage of HA that doesn't dissociate, no matter how strong.