the GT models from 94-95 came with one i believe, but not the cobra's. and like said above the 96,97 model cobras came with one but not the 98's. I remember reading somewhere that there wa sreason they didn't put them on, but can't think of the reason.
No 94-95 cobra came with a strut tower brace stock. I have talked to an engineer from ford about it right after I got my cobra (back in 2002). There wasn't one designed at the time to fit over/around the cobra intake. A couple of years later when the aftermarket was exploding with parts for the 94-95's. That is when several companies came out with strut tower braces for the 94-95 cobras.
I noticed a bit of extra vibrations with it off - nothing harsh, just didn't seem as rigid taking long sweeing fast turns, more flex I guess. Could have been all mental but I'm all for chassis support. I had the stock one on, ran a month without one, and then installed the MM a couple weeks ago.
If you guys want to improve handling on your lowered stangs, but a $15 pair of Swaybar Endlinks from Prothane or Energy Suspension. When you lower the car, you need to install shorter endlinks to restore the suspension geometry. I noticed a good difference after I swapped mine.
I bought mine from Arts Parts for cheap (a good guy). But I was told Auto Zone and other auto stores carry them as well.