I purchased a Supermicro board with a D-1541. Intel ARK specifies it has 16 threads (and if you click the question mark, it says that is per core). My Debian install shows 8 cores, 16 threads total. So is it really 2 threads per core?
The ARK page for the D-1541 says that it has 8 cores and 16 threads. Those numbers are for the overall package: the D-1541 has 8 cores, each of which can handle two threads, for a total of 16 threads. This matches what your operating system is telling you.
Where did you see that the Intel sites says it has 16 threads per core?