Well at least it's not home ground for any of them - I think that would make it worse. I guess you'll have perches fitted for the hens? As long as the ducks have enough room that they're not straight underneath the chickens, I imagine it'll be fine. As Mel says, might take a slight 'settling in' period. I've got a duck that goes into my chicken house at night but that's because she's still young and with her broody mum. I've tried moving her to the duck house but she doesn't like it and I've no idea whether she'll ever realise she's a duck!
H