The immediate reason for the warning is that it is calling query() without indication of whether it is a write query or not, thus requiring Rdbms to perform its legacy regexes on the SQL text to guess it.
However, more important than whether it passes the third parameter of query(), is that it calls query() at all, as this should not be used outside Rdbms internals. It exposes raw SQL and should be avoided in favour of safe interfaces like SelectQueryBuilder or IDatabase::select().
It is currently triggered approximately 100K/hour, making it the most common entry on the mediawiki-warnings dashboard in Logstash, across all MW channels and components. The instrumentation was added last month in https://gerrit.wikimedia.org/r/c/mediawiki/core/ /894110 to detect exactly this issue, on the assumption it will likely not trigger anything in production. Wikibase's use was one of two callers we found in production.
Wikimedia\Rdbms\Platform\SQLPlatform::isWriteQuery fallback to regex
#0 /srv/mediawiki/php-1.41.0-wmf.1/includes/libs/rdbms/database/Database.php(934): Wikimedia\Rdbms\Platform\SQLPlatform->isWriteQuery(string, integer) … #4 /srv/mediawiki/php-1.41.0-wmf.1/extensions/Wikibase/client/includes/Usage/Sql/EntityUsageTable.php(474): Wikimedia\Rdbms\DBConnRef->query(string, string) #5 /srv/mediawiki/php-1.41.0-wmf.1/extensions/Wikibase/client/includes/Usage/Sql/EntityUsageTable.php(407): Wikibase\Client\Usage\Sql\EntityUsageTable->getUsedEntityIdStringsMySql(array, Wikimedia\Rdbms\DBConnRef) #6 /srv/mediawiki/php-1.41.0-wmf.1/extensions/Wikibase/client/includes/Usage/Sql/EntityUsageTable.php(389): Wikibase\Client\Usage\Sql\EntityUsageTable->getUsedEntityIdStrings(array) #7 /srv/mediawiki/php-1.41.0-wmf.1/extensions/Wikibase/client/includes/Usage/Sql/SqlUsageTracker.php(273): Wikibase\Client\Usage\Sql\EntityUsageTable->getUnusedEntities(array) #8 /srv/mediawiki/php-1.41.0-wmf.1/extensions/Wikibase/client/includes/Usage/ImplicitDescriptionUsageLookup.php(303): Wikibase\Client\Usage\Sql\SqlUsageTracker->getUnusedEntities(array) #9 /srv/mediawiki/php-1.41.0-wmf.1/extensions/Wikibase/client/includes/Store/UsageUpdater.php(80): Wikibase\Client\Usage\ImplicitDescriptionUsageLookup->getUnusedEntities(array) #10 /srv/mediawiki/php-1.41.0-wmf.1/extensions/Wikibase/client/includes/Store/AddUsagesForPageJob.php(121): Wikibase\Client\Store\UsageUpdater->addUsagesForPage(integer, array) #11 /srv/mediawiki/php-1.41.0-wmf.1/extensions/EventBus/includes/JobExecutor.php(79): Wikibase\Client\Store\AddUsagesForPageJob->run() #12 /srv/mediawiki/rpc/RunSingleJob.php(77): MediaWiki\Extension\EventBus\JobExecutor->execute(array)