My Cougar had a vinyl top and in the sheet metal between the back window and the rear side window there are some good size holes for mounting the molding. If your was a vinyl top and some one used bondo to fill those holes then you could go around that area with a magnet. If they are filled with bondo there will be areas where the magnet pull is weak. As far as ther being a code, I don't know.
If the car had a vinyl top most times it has no drip rails
Im not sure if there is a way to tell if it was V-topped . I thought 65 tops were dealer added options but Im sure Im wrong . My original 65 had a vinyl top and under the top it was painted flat black .. I doubt you want to chip your paint to find out but if there is any paint areas around the windows you might be able to see if it has been covered over or not .
Hopefully someone will be able to tell you for sure .
Factory vinyl top cars had an aluminum strip riveted inside the rain gutter channel to secure edges. The rivet heads or holes where the rivets were previously should be visible from underside- looking up while getting into car (at least going from memory I believe they are visible and not covered by weatherstip or stainless channel below gutter).
There is several ways to tell if the car had a vinyl top. 65-68's have a chrome strip molding at the base of the B-pillar. I have seen many Mustangs with no vinyl top and have this molding making it obvious that it once had a vinyl top like your car. Another way to find out if your car has little holes in your drip rails. This is because these were holes for rivets to hold down a strip to hold the top to the drip rails. Another way to tell is your build sheet, possibly located around the wiring harness of the instrument cluster (I found my build sheet there). The build sheet will specifically tell you if your car had the vinyl top. My '68 is a vinyl top car and it's build sheet says so. I think but am not sure if the buck tag under the hood of your car has a code for this but the VIN# does not.
I suspect your car originally came with the vinyl top from the evidence of the B pillar molding alone. I say give it a vinyl top again. It is classy.