Even though they don't have the buckling issue I still use 1% as a minimum and design them as short columns.

The rationale for .5 comes from ACI 318 10.8.4 (if satisfied) - otherwise 1.

A pier/pedestal is still a short column and the 1% rienforcement rule applies.  However, jt12 is correct, treat the pier as architectural concrete and use the absolute minimum 0.5% since 10.8.4 states that the maximum reduction of section for architectural concrete is half the provided/original section, hence 1% goes to 0.5%.  You still need to check if the section can be treated as architectural concrete.  If the size of the pedestal for compression needed is larger than 0.5 x the pedestal provided, you have to use the ratio: 1% x (pedestal required by analysis) / (pedestal provided).  This will give you the amount of reiforcement for your short pier.

     No reinforcement is required for pedestals with the ratio of unsupported height to average least lateral dimension less or equal to three,(when designed as Structural Plain Concrete). ACI 318-05, 22.8

Structural Plain Concrete is ok as long as you don't have net wind uplift on the column -in which case, I'd not depend on the concrete tensile capacity.