Please see here on land administration during the early medieval period by /u/Morricane and here in which /u/Morricane and I describe the process by which the imperial family and nobility little-by-little lost their tax revenue.

During the Sengoku, the Imperial family and nobility survived on a combination of extreme cost-cutting (there weren't even formal empresses for many years), trying to get what little income they could from land, asking for donations from and selling ranks and titles to the warriors, and travelling the country to work as tutors of cultural pursuits to warriors eagerly wanting to imitate Kyōto's high culture and doing diplomatic work as nominally neutral third parties.

Nobunaga, Hideyoshi, and the first few Edo Shōguns "returned" or gave a lot of new land grants to the imperial family and nobility, and they basically survived on that income until the Meiji.