Most people I know charge by the number of stitches. as fleabag states I would check around & see what others are charging & go from there. *
I am fairly new to this so what I did was phone around my area and asked what other digitisers were charging and priced myself slightly lower.
Now I will just wait and see, with fingers crossed.
I think you also need to charge different prices for your won digitising and if you are merely stitching out existing designs.
Good Luck