Once you're at the point where you have to worry about these things, tuning the SQL is still probably much less complex than writing the query in your app language or figuring out how a NOSQL db can do these joins.
E.g., for a quick practice run, try optimizing Wordpress without making it a static page via caching - how many queries will you have to optimize and how much of a codebase rewrite will it be to make it significantly more performant?
the problem you describe is completely different and its more a measure of system health in its entirety of the DB. it can be easier to fix or harder depending on the precise cause. but that's a standard debugging skill which isn't strictly in the DBA skillset.