Same on my Chromebook Pixel LS too.
They were optional but now they added all kinds of additional mitigations and are also adding linux throttling and in the last 6 months or so I probably have gained ~60% compile time.
If lscpu still shows some offline cpus (let's say cpu 1 and 3 are offline), echo 1 >> /sys/devices/system/cpu/cpu<1 or 3>/online. Run lscpu again, and you should see all CPUs online and 2 threads per core.