As far as "honing" I think that the term should be cleaning really.
The only time I would "hone" with a ridgid type stone setup, is if there were significant pitting or rust on the surface of the bore to warrant refinishing the surface. Then though, there is the risk of oversizing the bore and losing the sealing ability. Be sure if you buy a wheel cylinder hone to get a good one. The "chatter hones" sold at most auto parts stores really don't do a very good job and unevenly remove material from the bore.
I ususally, if they aren't badly rusted, use a "brush type" hone which has the plastic stems with a small ball of abrasive on the end. These remove very little material and will leave a good cross-hatched surface for sealing the cup to the bore. They are usually finer grit as well for the reason mentioned above. These are similar to a "glaze-breaker" used on engine cylinders.
Ultimately if there is any doubt, just replace the wheel cylinders all together.