There isnt any way they "Server Sided" could really fix this, unless they disabled specific things via their manager all together, stall network, stall, exchange etc.
Anything Client Sided they could do (which they wouldnt know how), would be with ASM in the sro_client.exe, to stop players sending specific packets, however with Packet Injectors this would be useless. PK2 again is useless to this is just the content of everything, not to do with hard code.
I cannot really see much being done about it really, unless they watch ALL the accounts for obvious duping and a huge increase in Gold or Silk Items, which was not their before.
Or alternatively they could go through the itemdata.txt's in the database and Client and change all stackable values to 1 with certain items, with pots for example would suck ass.