HBaseStorageHandler skips rows with null valued first cells when only row key is selected.
HiveHBaseTableInputFormat.getRecordReader makes first cell selected to avoid skipping rows. But when the first cell is null, HBase skips that row.
http://hbase.apache.org/book/perf.reading.html 12.9.6. Optimal Loading of Row Keys describes how to deal with this problem.
I tried to find an existing issue, but I couldn't. If you find a same issue, please make this issue duplicated.