Debian not showing all cores?
If you scroll down on your CPU’s Ark page, you’ll see that it says
Intel® Hyper-Threading Technology ‡ No
Your CPU has six cores, but it doesn’t support hyper-threading, so your htop display is correct.
The CPU specifications on Ark show the full thread count, there’s no addition or multiplication involved; see for example the Xeon E3-1245v3 for a hyper-threading-capable CPU (four cores, two threads per core, for eight threads in total).
The ht moniker given to the underlying CPUID flag is somewhat misleading: in Intel’s manual (volume 3A, section 8.6), it’s described as “Indicates when set that the physical package is capable of supporting Intel Hyper-Threading Technology and/or multiple cores”. So its presence indicates that the CPU supports hyper-threads (even if they’re disabled), or contains multiple cores in the same package, or both. To determine what is really present, you need to enumerate the CPUs in the system, using firmware-provided information, and use the information given to figure out whether there are multiple logical cores, on how many physical cores, on how many sockets, etc. Depending on the CPU, a “CPU” shown in htop (and other tools) can be a thread (on a hyper-threading system), a physical core (on a non-hyper-threading system), or even a full package (on a non-hyper-threading, single-core system).
The Linux kernel does all this detection for you, and you can see the result using for example lscpu.
At least your CPU isn’t affected by any of the hyperthreading-related vulnerabilities!
In this context, "threads" is a synonym for "logical cores", i.e. total amount of logical cores, regardless of how many physical cores implement them. Not extra threads.
Your CPU has 6 logical cores, so booting Linux on it "sees" 6 CPUs.
Your CPU has 6 physical cores, so each logical core has a whole physical core to itself, rather than having a pair of logical cores sharing a physical core with Intel's SMT, which they call Hyperthreading.
I've used other Intel and AMD processors, and usually when the product says 6 cores/6 threads the total amount is 12
[citation needed]. Terminology like 2c4t (2 physical cores, 4 logical cores) has been standard for many years, across all architectures, not just x86.
I've never seen anything described as N "real" cores + N "extra" threads because that's not how it even works. Both logical cores are "symmetric", it's not like one had to be started up specially. They each act as full CPUs. (When one is in an idle deep sleep, the other one can go into single-thread mode and get all the execution resources. When both are asleep, the physical core can actually sleep)
Fun fact: OS support for hyperthreading lets the OS tell which logical cores share a physical core by reading CPUID data, and/or APIC / LAPIC interrupt-controller stuff. An OS that wasn't aware of hyperthreading would still boot up and see however many logical cores the CPU supports (HT was enabled in the BIOS), and I think everything would just work except that it might schedule 2 tasks onto cores that compete with each other for execution resources, while leaving other physical cores idle.
Some CPUs have more than 2-way SMT. e.g. Xeon Phi has 4-way SMT (4 logical cores per physical core) as a way to hide memory and ALU latency and get good total throughput without a lot of out-of-order execution resources.
IBM POWER uses 8-way SMT on big physical cores.