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The HBase shell help for the count command states:
Count the number of rows in a table. This operation may take a LONG
time (Run ‘$HADOOP_HOME/bin/hadoop jar hbase.jar rowcount’ to run a
counting mapreduce job).
Is it supposed to run this MapReduce job the normal way, via the JobTracker? Am I supposed to see it in the JobTracker history?
No. The hbase shell count operation is not using MapReduce- it is counting rows by advancing a cursor.
As the documentation that you posted states, run
Run '$HADOOP_HOME/bin/hadoop jar hbase.jar rowcountto run a counting mapreduce job