Question: Why is the D gene annotation missing in several TCR beta chains?
Answer: The key point is that the D gene is very short. Often during recombination it can get edited such that it isn't always recognizable relative to the germline sequence. Therefore, it is very hard to identify it during annotation.
Furthermore, the D gene is not very well annotated/represented in the reference. In the 10x GRCh38 V(D)J reference for human genome, (which was generated based on annotations from Ensembl), there are only 2 annotated genes for TRB, D-region, of which one is the 10x-curated annotation.
Below are these annotations. The length of the D genes in the table below are 16 bases for TRBD2 and 12 bases for TRBD1.