There was a tweet about what is seen by truesight. Jeremy Crawford's answer was:
Truesight—its definition (PH, 185) says what it does.
So, by definition, the Truesight says it allows you to "perceive the original form of a creature that is transformed by magic":
A creature with truesight can, out to a specific range,
see in normal and magical darkness, see invisible
creatures and objects, automatically detect visual
illusions and succeed on saving throws against them,
and perceives the original form of a shapechanger or
a creature that is transformed by magic. Furthermore,
the creature can see into the Ethereal Plane.
While the Devourer's victim is definitely transformed (their brains were replaced with a vile creature) by magic, its form wasn't changed, although (read - up to the DM) it is arguable what "form" is. Another tweet claims that truesight can't see through total cover:
Truesight pierces invisibility, illusions, darkness, and false forms. It doesn't pierce total cover
It is total cover what the Devourer has according to the Body Thief feature description:
While inside a creature, the intellect devourer has total cover against attacks and other effects originating outside the host.
So the Devourer inside a skull is safe.
The DM can say otherwise
For the sake of the plot, the DM can say that the victim is "tansformed by magic" enough to become noticeable for a truesight user. Is this ruling necessary, is completely up to the DM.