You can reason about what kind of device is this and in general basically look for statistical patterns. Which is what they seem to be pretty good at. If you have modified device then it's likely that you are an outlier.
Well I'm only thinking for a few seconds before writing a comment and they have some pretty smart heads working full time, but you could imagine compromising infrastructure of some popular app and adding your shiny bits there. The famous black box of radio also has some pretty decent hardware access. Gemalto sim cards hack etc.
When you help with some specific operation like drug trafficking you can probably limit amount of devices that you need to monitor by location. Then maybe deploy some zero cheaper zerodays there (or fivehundreddays, not everybody cares about the updates).
I agree that this is kind of paranoid talk. Maybe removing these parts does indeed help. If it does though, then I definitely wouldn't want to provide info about these modifications to the press.