Agreed. I couldn't turn on deduplication for radio IDs until recently, since dispatchers were on the analog side (and didn't have radio IDs) until the cutover. Now I'm afraid to turn it on since there is a risk of losing transmissions if one of the duplicates is on a talkgroup that isn't included in the stream. (An unlikely – but not impossible – scenario.)
I plan on digging into the dedupe code in SDRTrunk at some point and see if I can make the radio ID dedupe a little better, so that there isn't the risk of losing transmissions. Once I feel that it can be trusted to not miss anything, I'll turn it on.