Not sure about Zoysia but my Paspalum i cut at 1" is very very thick. I have a small patch that i have to cut at 1.75" and like yours can part it and see ground. I think that is how most runner type grasses act.

I think that is how most runner type grasses act

No, that isn't normal for Zoysia. It is almost all stem, with blades of grass only at the last inch or so. It isn't supposed to be like that.

I'm also in central Florida and have a back yard of Zoysia, my third house with Zoysia. I cut my grass weekly during the growing season to about 2 1/2 inches. The University of Florida recommends 1/4 to 2 1/2 inches but depends somewhat on the variety of Zoysia. If your grass is healthy it will probably survive okay. But if you suspect that it is not healthy then it could get hit in the fall or winter by insects e.g., billbugs, mole crickets; or by fall/winter fungus and disease. A final guess -- if your fertilizer contains excessive nitrogen, the leaves will grow but the roots and stems may be at risk.
University of Florida info: http://edis.ifas.ufl.edu/lh011
University of Georgia info: http://www.caes.uga.edu/publications/pubDetail.cfm?pk_id=6884

I am having the same problem cutting at 3" and I am slowly working it down to 2 1/4". I have to cut 1/4 - 1/2 inch lower the first time or it looks brown every time I cut it, for a few days. In the walkway spots the grass is about 2" and is green all the way down.

My question was: if I cut the grass, this winter when it is dormant, short enough so that there is only stem left, will it come back?

Again, only about the top 3/4 to 1" is blades of grass. Everything below that is stem.

I would continue to cut at the same level as you have been doing. Since you are in zone 9 there are many growing days left before you get a hard frost or freeze. To remove all of the blade before it occurs might cause the grass to lose its resistance to freeze or pests.
Not mentioned - whether you periodically measure the height of the cutting blade.

Hi,

Wondering if your Zoysia flourished after some time and a much lower cutting height?

Thanks!