Given the marketing toward HPC tasks, shouldn't hyper-threading be disabled?

No? We make sure that pairs of vCPUs (hypertwins) stay together. If you'd like, you can offline your threads in the guest for a fairly similar outcome. Some of us regret that we sell an n1-standard-1 and the shared core machine types, but it's pretty nice to have a $5/month VM price point for those that want it. Most folks doing serious numerical computing end up using much larger VMs, and always crossing NUMA nodes (which is a much larger impact).

Disclosure: I work on Google Cloud (and historically focused solely on Compute Engine).

I'm curious, what is there to regret about having a shared core machine type? Some people have a use for them and appreciate the cost savings.

Disabling hyper-threading only makes sense if you're getting messed up by the OS's scheduler.