To my experience, SCSI controllers usually last MUCH longer than mainboards - what if you decide to swap mainboards next year? U160 SCSI will still be a good technology then ...
So get a normal mainboard and a neat dual channel SCSI controller like Tekram's 390U3W. That way you get one fast U160 channel for HDDs and tapes, plus one legacy UW/U channel for your other peripherals.
The other drawback of onboard SCSI is that it usually doesn't come with all the cables and slot brackets you'll need, and these add quite a lot of cost.
That said, I've seen a couple of really good bargain offers on the K7Master-S board. OK, it's an old chipset, but if you're sure you'll never upgrade that box after building it, then it's worth thinking about.
regards, Peter