This is application dependent. In Virtuoso, SPARQL and SQL share
the same query execution engine, query optimizer, and cost model.
If data is highly regular (i.e., a good fit for relational
representation), and if queries typically access most of the row,
then SQL will be more efficient. If queries are unpredictable, data
is ragged, schema changes frequent, or inference is needed, then
RDF will do relatively better.
The recent Berlin SPARQL Benchmark shows some figures comparing
Virtuoso SQL and SPARQL and SPARQL in front of relational
representation. However, the test workload is heavily biased in
favor of relational. See also BSBM: MySQL vs Virtuoso.
With the TPC-H workload, relationally stored data, and SPARQL
mapped to SQL, we find that with about half the queries there is no
significant cost to SPARQL. With some queries there is additional
overhead because the mapping does not produce a SQL query identical
to that specified in the benchmark.