Indexing every WHERE column?
Turn on those flags only for initial development.  They are too noisy with false alarms otherwise.

There are valid cases for queries that do not use indexes.

There are cases (such as EAV) where it is impractical to have indexes for every possible query.

I prefer to turn on the slowlog with a low value for long_query_time, and later gather what queries are the "worst".  This is a much better list of queries to work on improving.  It may include some slow queries with the best possible index, and exclude some very fast queries that don't involve any index.

Do not blindly index every column.  Learn about "composite" indexes.

See my Cookbook on creating optimal indexes for basic queries.