It seems there are mode-S radars immune to ID duplication effects. In the technical specifications of a national Thai tender for six sites (2012) the following requirements were stated:
1.1.1.26. The SSR Mode S System shall track all the aircraft, including aircraft with duplicated addresses and maintain the roll-call list.
1.1.1.12. The non-unique address Mode S targets shall be flagged in the ASTERIX data item I048/030 Warning Error/Conditions code 16 “Duplicated or Illegal Mode S Aircraft Address”.
http://www.aerothai.co.th/thai/anou_...3771850077.pdf
http://www.aerothai.co.th/thai/anou_...3714470079.pdf
I guess it's a very sensitive issue which radar models are immune and which are not.