It would certainly be grammatical, and to my ear, more idiomatic to have written
He must, he thought, have been ten or eleven years old when his mother disappeared.
Obviously there is no question of a sequence of events here because the point is to assert their simultaneity.
I hesitate to say it is ungrammatical because the mother did not disappear every day for two years. That is, for at least part of those two years, the mother had disappeared. This may be one of those sentences where intent tripped over syntax and what was meant is actually something like
His mother must, he thought, have disappeared a year or so after he had turned 10.
There the past perfect is fully justified though not completely necessary because the "after" alone makes the sequence clear.