Mid 2010 MacPro 5,1 Hyperthreading issue

There is no BIOS per se in macOS. You can get access to the kernel that is running things directly using Terminal. Your 'Muti-threading disabled' theory is far-fetched.

To see that is rarely going on, Consider downloading and running this little "discovery" utility, Etrecheck. It changes NOTHING. Etrecheck was developed by senior contributor here, and uses system calls to collect often-needed information.

it contains little tests for speeds of devices, CPU utilization, memory usage, energy usage and a digest of recent problems, in one easy to use package. it does not even need to be Installed. Because less can be learned when your Mac is running great, best time to run is when your problems are actually occurring, if possible.

if you follow the directions faithfully, its report (pre-laundered of all personally-identifiable information) can be "Shared" to the System ClipBoard, then Pasted into an ‘Additional Text’ window in a reply on the forums.

 Use Etrecheck Pro for free:

http://Etrecheck.com

the start a reply of the forums, use the Additional text Icon, and PASTE the result:

,,,

having hyper-threading 'accidentally' disabled has NEVER been reported as an issue here.

Poor performances has, LOTS of times. but it is not down to CPU cycles alone. The most impactful items are:

By far the easiest way to cause poor performance, instability, overheating and crashing is to install ANY third-party speeder-uppers, Cleaners, Optimizers, or Virus scanners, Bit Torrent, or a VPN that you installed yourself.

The next most common way to cause poor performance is to have one Boot drive that is very slow, and use it for everything. Savvy video editors figured out early-on that the right way to set up your driveS was to have a boot drive that was 'as fast as you wallet could go', a separate sources drive, a separate destinations drive, and if your workflow has libraries or scratch files, a separate Scratch drive.

Rotating magnetic drives, if selected carefully, can attain as high as 150 M bytes/sec steady state.

If Drive SPEED is what you seek, there are Solid State Drives SATA SSD drives you could install in a Mac Pro 5,1 silver tower drive bay for comparable amounts of money that can attain nominal 550 M Bytes/sec speeds, about 10 times faster than the fastest Rotating Magnetic drives. 

Next higher is a simple x4 PCIe card (under US$30 for the empty card) that could provide nominal 1500 M Bytes/sec in your Mac Pro 5,1 in a PCIe2 x4 slot. Installation is slightly more complex, because you must apply a heat transfer pad to the SSD stick and bolt on a heatsink (included in the kits).

Somewhat more complex and far more expensive are PCIe card with x8 or x16 capability. The Mac Pro does not support ‘bifurcation’ (i.e., writing to each x4 of an x8 slot separately) so a complex full-width drive controller chip on the card is required. This makes x8 cards far more expensive than x4 cards, and x16 cards more expensive still. But possibly twice as fast or more.

in your case, with no internet connection, you could PASTE into TextEdit document, save that to a USB stick, and carry the USB stick to another Mac for uploading.

do you have TRIM enabled on your third-party SSD drives?, If not, these drives can not unload their deleted data, and eventually, they fill up with deleted data (undetectable through standard MacOS) and write speeds slow to almost nothing.

Does the drive test show at least your boot drive as appropriately fast?

Do you have the appropriate amount free space on the boot drive? one large App could launch and demand 64 GB (which could spill into that much Swap file space) in a very small amount of time. if it did not crash, it would run a drive with only about that amount of free space into a very spectacular out-of-system-storage crash. These are very difficult to recover from.

Is ALL the RAM you paid for showing up as present and working? in this model Mac, RAM failures at startup can declare large swaths of RAM slots "empty".

¿what is the date of your most recent backup, and by what method?