Does transcription terminate at the end of antibiotic resistance genes on the Duet expression plasmids?
Generally they do, however this is often doesn't completely stop transcription run-through.
Note that in a T-7 reaction there shouldn't be any transcription of the Amp or Kan genes as these are run off promoters that  the T7 phage RNA polymerase won't be able to transcribe off as it is extremely specific for the T7 promoter.
The solution if you are really worried is to linearize your plasmid immediately downstream of your terminator but before the AMPR gene using a restriction enzyme with a single cut. This will also give you a specific size sequence being transcribed, which is very useful if you are determining copy number in say a qPCR.