At which URL did you encounter the problem?

https://finto.fi/kauno/fi/page/p4610

What steps will reproduce the problem?

1. Go to URL above
2. Observe hierarchy
3. Also true if one refreshes with the broader concept

What is the expected output? What do you see instead?

As it stands in the wiki, it should be enough to have owl:deprecated true set to a concept (and it is, indeed, set, as the Skosmos is displaying a warning for it) for it to be not shown on the hierarchy if the skosmos:showDeprecated predicate is not used (it is not for this vocabulary). However, the deprecated concept can not be found via alphabetical listing nor search so those two are working.

Compared to https://finto.fi/kauno/fi/page/p1122 (that is working), it seems like the difference is in stating of skos:topConceptOf and skos:hasTopConcept predicate triples; stating skos:inScheme (to other concept scheme) in itself is not enough.

To conclude: either the wiki documentation is wrong or there is a problem in code unrelated to data problems which are apparent.