Perhaps the reason for raiding the employees' homes is to gather evidence of full-time work for a single employer, as well as what they gather from Ryanair.
A corporation might well hide that information at head office, but an individual is more likely to keep it in their house, and a copy of a flying schedule, any payments, etc, will be evidence whether obtained from the pilot or Ryanair. Meanwhile, to try to prove that Ryanair is operating pilots as individual full-time subcontractors working only for Ryanair, the authorities would need to show they had tried to find evidence of this person working for anyone other than Ryanair and had not found it.
So the German authorities might well raid some pilots' houses without being after the pilots, although clearly that doesn't make it any nicer for the pilots.