The good thing is that the acidity of base and crystal malts is somewhat close when the malts have similar color. If the honey malt is a minor component of the grist, I think you will find that it only makes a few hundreths difference in the pH estimate. It could be on the order of a tenth difference, if the honey malt percentage is high.
I don't know how to classify honey malt, but I am inclined to say it has been stewed to some degree to create that unique sweetness and that implies a crystal malt.