Rogues shouldn't be spawning on those maps if you've set those values to 0. You can check the _waves.json files for each map inside of your donottouch/debug folder to see precisely what types of bots are being spawned: exUsec means rogue, and pmcbot means raider. Are either of those appearing in your _waves.json files?
I checked the waves file for the maps I was in, only assault and assaultgroup show up. However, I checked the bosses folder and it seems that on woods there's a 30% chance for exUsec to appear? That might explain why i'm seeing them in woods, though I swear I saw them in customs too but my memory is a bit fuzzy.
If the "bosses" chance in debug is the reason i'm seeing rogues, how do I safely edit/disable this?