Nanostructuring of graphene is in part motivated by the requirement to open a gap in the electronic band structure. In particular, a periodically perforated graphene sheet in the form of an antidot lattice may have such a gap. Such systems have been investigated with a view towards application in transistor or waveguiding devices. The desired properties have been predicted for atomically precise systems, but fabrication methods will introduce significant levels of disorder in the shape, position and edge configurations of individual antidots. We calculate the electronic transport properties of a wide range of finite graphene antidot devices to determine the effect of such disorders on their performance. Modest geometric disorder is seen to have a detrimental effect on devices containing small, tightly packed antidots, which have optimal performance in pristine lattices. Larger antidots display a range of effects which strongly depend on their edge geometry. Antidot systems with armchair edges are seen to have a far more robust transport gap than those composed from zigzag or mixed edge antidots. The role of disorder in waveguide geometries is slightly different and can enhance performance by extending the energy range over which waveguiding behavior is observed.