99 cobra cooling system hole?

Yes, that is usually referred to as the coolant crossover tube on our cars. The hole should NOT go all the way through! It looks like it corroded through - that is a good spot to add a water temperature gauge
(see link: http://home.flash.net/~ivc1/cobra/tmpsensr.html )

The depression is there so you can unbolt it with a 1/4" drive in order to refill the cooling system after flushing it (you would add coolant into this hole because it prevents "air bubbles" from entering the system).

I *think* you can purchase this cap separately now, but you might want to check with your parts department first (if they won't sell it separately, ask for the same part for the Marauder - I have read that it is an exact duplicate if you need a new one).
Or you could always look for a junked vehicle and take the cap/fitting or buy a fitting at a hardware store...g'luck.

It doesent go all the way through. Its so you can unscrew that cap and let the air out of the coolant system. Touch it up with some paint.