Yes, you can cut the top of your 'Shimpaku'.
What this will do is another matter.
You are unclear about the effect this had on your J. squamata.

Oh, dear, and I thought I was making sense.
No, I have no intention of cutting the top off the Shimpaku. It is styled the
way I want it. What I meant was, can I treat the Shimpaku like a subtropical,
give it about 2 months of dormancy, and then put it under the fluorescent
lights until spring? My teacher says no, it has to spend the whole winter in
the cold sunporch & then go outdoors in the spring. I would like to know what
the physiological difference is between the two species.
Since the J. squamata has only been in the ground one season, I can't see much
effect yet. I know it will eventually thicken the trunk. The remaining branches
will continue to grow. Of course I won't know the exact outcome for a couple of
years, but that does not concern me.
Iris,
Central NY, Zone 5a, Sunset Zone 40
"If we see light at the end of the tunnel, It's the light of the oncoming
train."
Robert Lowell (1917-1977)