I'd say that using distributed computing engines like Apache Hadoop or Apache Spark imply basically a full scan of any data source. That's the whole point of processing the data all at once.
HBase is good at cherry-picking particular records, while HDFS certainly much more performant with full scans.
When you do a write to HBase from Hadoop or Spark, you won't write it to database is usual - it's hugely slow! Instead, you want to write the data to HFiles directly and then bulk import them into.
The reason people invent SQL databases is because HDDs were very very slow at that time. It took the most clever people tens of years to invent different kind of indexes to clever use the bottleneck resource (disk). Now people try to invent NoSQL - we like associative arrays and we need them be distributed (that's what essentially what NoSQL is) - they're very simple and very convenient. But in todays world with SSDs being cheap no one needs databases - file system is good enough in most cases. The one thing, though, is that it has to be distributed to keep up the distributed computations.
Answering original questions:
These are two different tools for completely different problems.
I think if you use Apache Spark for data analysis, you have to avoid HBase (Cassandra or any other database). They can be useful to keep aggregated data to build reports or picking specific records about users or items, but that's happen after the processing.