It depends what you are doing whether you can utilise all 12 cores & what your requirements are for single threaded performance. The single threaded performance of the cMP is well down on that of more modern CPUs. Looking at single core Geekbench results a 3.33GHz cMP scores 2739 (extrapolating a 3.46GHz would score 2846) whereas a 12-core 2.7GHz nMP scores 3139. A 6-core 3.5GHz nMP scores 3596.My 4,1 2009 MacPro smokes a fully loaded 6,1 2013 nMP.
With 12 cores at 3.46GHz, 96GBs RAM, the Squid which holds four SM951s in a RAID 0 in PCIe slot 2 (5700MB/s reads) and a total system cost of less than $2800 (including a couple 3TB HDDs), and a Geenbench 3 64-bit score of 32000, I got two of them! For the cost of one 12-core nMP you could buy FOUR modded 2009s.
There is then the small point of warranty & service on an old machine versus a new system although warranty might be moot if you have there backup systems sitting on the shelf