So if i'll sum it up, in case of a hardware failure, let's say a dead motherboard, the minimal downtime will be if i happen to have a spare system or at least a spare MB that supports ECC memory etc that i can transfer my FreeNAS to.
Until i buy a new motherboard.
This solution cost money and takes time when i compare them to a failing RAID 1 array on NTFS. For example, i once had an m1015 who died on me. All i had to do is to plug the HDD's to the MB instead of the card and i had access to everything, no downtime at all.
That is something to consider indeed.
That is not a fair comparison. You are speaking of a faulty MB; which in any case (if you had a HBA or RAID Card) would result in the same thing... Having to replace the MB.
To make it fair say the HBA Card died, then you would simply just replace the HBA Card and you are back in business. Or if you had the free SATA ports on the MB, you could simply plug the drives directly to the MB and be back up and running as well.
As long a FreeNas has direct access to the drives it doesn't really care about the method it uses to get to them (SATA Port, HBA, even USB <--- NOT Recommended)...
Now to go even further, say you had a hardware Raid5, Raid6, etc.. How does your scenario work out then? It doesn't.... However with FreeNas it would be perfectly fine with RaidZ1, RaidZ2, etc.
Don't get me wrong Hardware Raid does have it places, but to me it pales in comparison to what FreeNas/ZFS is capable of.