Yes, any socket 1150 motherboard will be compatible with the Xeon E3-1231v3 as long as the BIOS is updated (on the elder 8 series chipsets, e.g. H87 etc.). Since this is regarding a H97 motherboard, it'll most likely be compatible without a BIOS update due to the H97 being more recent.
Hyper Threading does not require a "special" motherboard; it's simply a feature the processor provides.
All the best.