While I can see how Art could have not included Anja's story due to risk of poor portrayal of his mother and her story I feel it may have been to show his fathers care for his sons future. IThat Art wished to show his fathers actions towards his son? That maybe Vladek wanting to try and push Art father rather then have him dwell in the past was the reason for the lack of story surrounding Anja?
I feel this is seen in how at the begining Vladek starts by telling of how he and Anja met but as the story continues i feel Vladek begins to ralise that Art must move forward in his own life and not concentrate on his father's. This is seen in how Vladek throws out Art's coat to symbolize getting rid of the past and eventually when we learn that Vladek burned Anja's journals.
Finally could Vladek have have burned the journals as an attempt to protect his son not only from the truths about Anja's struggles but also to keep his son moving forward in life rather then trying to go back?