In Harry Potter and the Goblet of Fire, Snape says:
“You know I’m hiding nothing, Moody,” he said in a soft and dangerous voice, “as you’ve searched my office pretty thoroughly yourself.”
Moody’s face twisted into a smile. “Auror’s privilege, Snape. Dumbledore told me to keep an eye —”
“Dumbledore happens to trust me,” said Snape through clenched teeth. “I refuse to believe that he gave you orders to search my office!”
Therefore, why didn't Snape question Dumbledore why he let "Moody" (Crouch Jr.) search his office?
We know he had the opportunity to speak to Dumbledore privately (and was on close enough terms with him to be able to ask if he gave "Moody" the order since they were discussing his Mark) around this time. From The Prince's Tale in Harry Potter and the Deathly Hallows:
A whirl of color, and now everything darkened, and Snape and Dumbledore stood a little apart in the entrance hall, while the last stragglers from the Yule Ball passed them on their way to bed.
“Well?” murmured Dumbledore.
“Karkaroff’s Mark is becoming darker too. He is panicking, he fears retribution; you know how much help he gave the Ministry after the Dark Lord fell.” Snape looked sideways at Dumbledore’s crooked-nosed profile. “Karkaroff intends to flee if the Mark burns.”
“Does he?” said Dumbledore softly, as Fleur Delacour and Roger Davies came giggling in from the grounds. “And are you tempted to join him?”
“No,” said Snape, his black eyes on Fleur’s and Roger’s retreating figures. “I am not such a coward.”
Obviously, there is an out-of-universe reason for Snape not asking Dumbledore, as Dumbledore would've then realized "Moody" was an impostor before Rowling wished to reveal this to the reader.
However, is there an in-universe reason Snape never asked Dumbledore?