+1 on what Victor said - if you have diverse RF environments, certainly makes sense to group the APs based on that as a minimum to aid for tuning of RF related things. Even if you consider the RF to be fairly constant, it can make sense to group APs based on something geograhical - can maybe be used later in radius policy since ap-group is sent up as a VSA.
We have some customers that have pushed the number of groups pretty high, well into the 100+ category, you are unlikely to run out of config space (but it can be a challenge for smaller/older controllers).
if you can navigate your way around a bit of basic shell scripting, you can quickly and easily handle the additional work required if you have to make changes to many ap-groups.
regards
-jeff