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You're not supposed to have levies raised unless you're using them; disbanding levies in peace time will drastically reduce the maintenance cost of your armies (since you'll only be paying for your retinue + mercs).

Additionally, I believe vassals contribute a drastically reduced (maybe zero?) percentage of their income if they aren't making a whole lot to begin with. It's to encourage you to spread your kokujin titles out instead of giving only one to each vassal.

Yes, there's a basic deduction before a percentage is paid. Small vassals will usually not contribute anything since they usually upgrade their one or two provinces.