I believe it is intentionally left vague.
What we know is the following:
The body of Amicia and Hugo's father Robert de Rune is initially untouched, until it is discovered by Amicia and Lucas in Chapter 12: 'All That Remains'.
It is remarkable that at that point the rats seem to develop a technique to breach the metaphysical barrier that kept them at bay.
What's more is that we don't find out what exactly happens to the body: it gets engulfed by rats, and All That Remains is shifted ground, almost like a burial mound, and Amicia lamenting:
"They took his body. They took him from me!"
There are a few bodies in the kitchen and adjacent rooms that have remained unscathed as well: these are bodies of servants of the De Rune family.
Another remarkable fact is that the room where Hugo - the carrier of the Prima Macula - spend most of his life remains perfectly intact as well.
More people have wondered why some of the bodies were still intact and come up with some theories:
- According to a Reddit user it has to do with the bond between Hugo and others. If it was strong, such as with his parents and some servants, their bodies remain untouched because subconsciously Hugo forbids the rats from eating them.
Interesting, but there are some problems with this: as Amicia you constantly need to actively fight or avoid the rats. Even though Hugo might not have known her very well, there is no reason he would allow the person who protects and guides him to suffer this terrible fate.
- This is somewhat reinforced by a late entry in this Reddit thread.
So barring any official lore, I think the closest we can get to a reason some bodies were not devoured, is that whatever Hugo has a sentimental connection with — i.e. explicitly not a conscious connection with — remains intact: his room entirely, and the few servants he likely had interactions with.
This would explain why Amicia is still getting attacked. Additionally, it would offer yet another profound aspect of the titular 'innocence'.
I also think it's more logical that Robert de Rune's body has remained intact because he carried a latent or recessive version of the ancient Prima Macula curse, not because he was close with Hugo. This could also account for the rats burying him, as if to preserve his body.