Short answer first: No, Mainboards dont have a standard port for disk controllers.
Nor do cases have a standard slot for disks.
In case your server actually accepts SATA or SAS disks in the slots, you have to check what kind of slots are on the mainboard (PCI, PCI-X, PCI-E). Then you can choose a extension card for your server. You might go for a simple SATA-card with no raid functions, and do RAID with the OS. Or go for a good RAID card to do the raid for you. Dont buy a cheap raid card: they are driver based anyway, and they only "promise" to work, if you get my drift.
IMHO, the ideal household NAS server is silent. Your heirloom server is not going to be silent. And it will use a lot of electricity. 200W or so is a lot in a household. You would notice that on the bill. Aim for 30W - 50W and do the math on cost for an additional 150W per year.
How about you look into some of the modern, cheap NAS enclosures? (Buffalo Linkstation comes to mind)
Or a cheap 1 GHz-like PC, Atom or not, and maybe use FreeNAS or similar for it?
My household server lives in an old midi tower, with a fanless atom board and 2x 500 GB SATA. Quiet, cheap, big enough.