I will disagree with Todd here. Voucher tenants can be a great opportunity, but you need to be smart about it like you would with any other rental property. I have found that in certain areas it's possible to get better rents with vouchers than you would without, especially if you target certain unit types that are in high demand by AHA (see number 2 below). My experience with the tenants in my voucher units has been great so far. You can screen them just the same as you would anyone else without a subsidy, and you even have some extra protections since AHA will inspect your properties regularly at no charge. Just screen your tenants well, and use a strong lease document - again like you should anyway. To answer your questions:
1. Ways to section 8 proof property to limit costly damages (ie: removing carpets or high priced appliances?)
Same things you'd do on any lower-tier property. I usually try to avoid providing washer/dryer, and will use pretty standard appliances. If there is already carpet I won't pay to have it removed unless AHA tells me to (this would only happen if it was in really bad shape already). Once it reaches the end of its life I'd probably opt to replace with some kind of vinyl.
2. What is the most desirable type of property for section 8 ? (2bd, 3bd, 4bd ? )
In my opinion, 4bd since they are very rare and in high demand. Last year I bought two 4bds and in my talks with AHA learned there was a long wait list for these types of units and thus I was able to negotiate better rents.
3. Easiest housing authority district to deal with in Atlanta metro area (if there is such a thing)
No such thing. AHA covers all of City of Atlanta. Other municipalities have their own housing authorities. I only buy in Atlanta proper.
4. Any things you know now that you wish you knew in the beginning with investing with Section 8?
It's very helpful to have a property manager that is used to working with AHA since there are some quirks (inspections, standards). Rent negotiations with AHA can be a bit of a hassle, but you will quickly learn how to navigate this. Finally, if you are considering accepting voucher tenants start the process of getting certified with AHA as a landlord early. It can take a while, especially if you're located out of state (like I am).