Did you ever notice how often Troi could short-circuit an entire episode because she would have just been able to "sense" what's going on? For instance, in "Conspiracy" where a bunch of high ranking Star Fleet officers are compromised by a parasite... she never detects anything wrong.
In the episode where Data is kidnapped, again, Troi is conveniently not able to sense anything.
The episode where Picard is replaced with a doppelganger (which acts pretty differently from him, for example, drinking with the crew) she senses nothing.
I don't know if the writers forgot she exists or what.