What kind of braking will you be doing? Mostly street? Road racing? Autocross? Mixture of racing and street?
If you want durability and solid performance for the street, factory Ford/Brembos are plenty rotor for the vast majority of cobra owners out there. You can usually find good prices on them at Tirerack or other similar vendors.
If you plan on seriously open tracking your cobra (ie - roadrace or autocross events), you may even want to explore upgrading your entire brake package. The typical big name players in the brake industry all have kits out there (you can Google for those manufacturers; I don't know how reputable R1 concepts' brake hardware is though, so buyer beware).
Keep in mind that many people simply like the cross drilled, zinc, slotted, etc, etc rotors for "looks" as well. If you want rotors to look "good," well then by all means go for them - I'm not knocking these types of rotors. The ones that aren't junk, may offer some performance improvement over factory brakes, but they may come with added noise, brake dust, and potential problems. You may find a few "cross drilled" rotors developing hairline cracks from basic street usage.
If your cobra just needs some TLC in the brake department, I'd recommend bleeding your brake fluid, adding stainless steel brake line/hoses (front end at the very least), new pads (brake pad manufacturer is another can of worms, lots of opinions on them), and possibly just turning your original rotors (if enough material is there and/or they are not warped). If new rotors are needed, purchase accordingly.
Whatever route you choose, be sure to do your research first.
G'luck and welcome aboard (see that you are new to Stangnet).
