It is unknown whether Mad Eye Moody was visible on the map even when he was hidden in his trunk. Still if he was it is completely plausible that Harry just ignored seeing him since the trunk was in the DADA teacher room, where Mad Eye was expected to be.

In more detail:

First of all Harry does not look at the map all the time. He used the map more often during his sixth year but before that he only checked on it when he wanted to have a clear path during the night.

Even if Harry took a look at the map and saw Mad Eye Moody, so what? He wasn't on a place where one would not expect to find him. Exactly the opposite - he was in his room.

He could have seen BOTH Barty Crouch Jr. and Mad Eye in the room but this is also not something unexpected or too unusual. The map only shows "Barty Crouch" and Harry could assume that Barty Crouch Sr. is just visiting Moody for some reason.

It would have been suspicious to see Mad Eye in his room under following circumstances:

• in class when Harry sees fake Mad Eye in front of him
• during eating times in the Great Hall when fake Mad Eye is there

Still this never happens. The DADA lessons are interesting enough to keep Harry from looking at the map and the Great Hall is too crowded and Harry keeps the map a secret so he does not want to show it to everyone.

It is unknown whether Mad Eye Moody was visible on the map even when he was hidden in his trunk. Still if he was it is completely plausible that Harry just ignored seeing him since the trunk was in the DADA teacher's room, where Mad Eye was expected to be.

In more detail:

First of all Harry does not look at the map all the time. He used the map more often during his sixth year but before that he only checked on it when he wanted to have a clear path during the night.

Even if Harry took a look at the map and saw Mad Eye Moody, so what? He wasn't on a place where one would not expect to find him. Exactly the opposite - he was in his room.

He could have seen BOTH Barty Crouch Jr. and Mad Eye in the room but this is also not something unexpected or too unusual. The map only shows "Barty Crouch" and Harry could assume that Barty Crouch Sr. is just visiting Moody for some reason.

It would have been suspicious to see Mad Eye in his room under following circumstances:

• in class when Harry sees fake Mad Eye in front of him
• during eating times in the Great Hall when fake Mad Eye is there

Still this never happens. The DADA lessons are interesting enough to keep Harry from looking at the map and the Great Hall is too crowded and Harry keeps the map a secret so he does not want to show it to everyone.