The perks (when not a buff) are just flags, markers. They just say that the job has that, but it is up to some other code somewhere to check it and take an action or do something with it.
In that case, this function
local num_to_spawn = 1
--If the this entity has the right perk, spawn more than one
local job_component = entity:get_component('stonehearth:job')
if job_component and job_component:curr_job_has_perk('farmer_harvest_increase') then
num_to_spawn = 2
It checks if the guy harvesting the crop has the perk, and if it has spawns the item twice.