Insignia is something of a sore point. Apparently many of the newer HTL models and/or some SCP feature has broken them, and there's an almost pathological refusal to fix insignias for some reason I honestly cannot fathom.
I fixed insignias for all HTL ship for me. Can't stand being without insignia.
It's actually a easy fix.
Open the ship you want to fix in PCS, look up the insignia tab and for each insignia, increase the offsets X coordinate by approximately 1.
That should fix it, assuming that the model has allready imported insignia from the stock model. If not, you'll have to first import the insignias and then increase the offset.
This happened becouse the HTL models have more detail and are generally a bit wider, so the insignia ends up under the hull...
Note that for some ships it won't look good again. Some HTL models now have rounded surfaces or intrusions/extrusions where the insignias ought to be on the original model.