PropertySuggester on wikidata.org does not treat P279 as classifying, while the suggester data is generated under the assumption that P279 is classifying. This inconsistency may lead to sub-optimal suggestions on Items that use P279.
PropertySuggester's extension.json sets PropertySuggesterClassifyingPropertyIds to [ 31 ]: https://github.com/Wikidata-lib/PropertySuggester/blob/master/extension.json. Configuration for the live site does not override this, see https://phabricator.wikimedia.org/source/mediawiki-config/browse/master/wmf-config/Wikibase-production.php (it only overrides it for test.wikidata.org). Or we may test this on the live site first, before changing the defaults.
However, PropertySuggester-Python's analyzer.ini sets it to 31,279, see https://github.com/Wikidata-lib/PropertySuggester-Python/blob/master/propertysuggester/analyzer/analyzer.ini. A look at the wbs_propertypairs table confirms that this configuration is used to produce the data for the live site.
Add 279 to PropertySuggesterClassifyingPropertyIds in PropertySuggester's extension.json. This makes the default config consistent, and it causes the life site to treat P279 as classifying, allowing it to use the data in wbs_propertypairs correctly. Settings for labs and test should be adjusted accordingly. We may want to test this on the live site first, before changing the defaults, though.
We could also do it the other way around by removing 279 from analyzer.ini, but that would require the data to be re-generated. Also, treating P279 (subclass of) as classifying seems sensible.