Hi Markus,
You asked "who is creating all these [subclass of] statements and how is this done?"
The class hierarchy in
http://tools.wmflabs.org/wikidata-todo/tree.html?q=Q35120&rp=279&lang=en shows a few relatively large subclass trees for specialist domains, including molecular biology and mineralogy. The several thousand subclass of 'gene' and 'protein' subclass claims were created by members of WikiProject Molecular biology (WD:MB), based on discussions in [1] and [2]. The decision to use P279 instead of P31 there was based on the fact that the "is-a" relation in Gene Ontology maps to rdfs:subClassOf, which P279 is based on. The claims were added by a bot [3], with input from WD:MB members. The data ultimately comes from external biological databases.
A glance at the mineralogy class hierarchy indicates it has been constructed by WikiProject Mineralogy [4] members through non-bot edits. I imagine most of the other subclass of claims are done manually or semi-automatically outside specific Wikiproject efforts. In other words, I think most of the other P279 claims are added by Wikidata users going into the UI and building usually-reasonable concept hierarchies on domains they're interested in. I've worked on constructing class hierarchies for health problems (e.g. diseases and injuries) [5] and medical procedures [6] based on classifications like ICD-10 and assertions and templates on Wikipedia (e.g. [8]).
It's not incredibly surprising to me that Wikidata has about 36,000 subclass of (P279) claims [9]. The property has been around for over a year and is a regular topic of discussion [10] along with instance of (P31), which has over 6,600,000 claims.
You noted a dubious claim subclass of claim for 'House of Staufen' (Q130875). I agree that instance of would probably be the better membership property to use there. Such questionable usage of P279 is probably uncommon, but definitely not singular. The dynasty class hierarchy shows 13 dubious cases at the moment [11]. I would guess less than 5% of subclass of claims have that kind of issue, where instance of would make more sense. I think there are probably vastly more cases of the converse: instance of being used where subclass of would make more sense.
As you probably know, P31 and P279 are intended to have the semantics of rdf:type and rdfs:subClassOf per community decision. A while ago I read a bit about the ELK reasoner you were involved with [12], which makes use of the seemingly class-centric OWL EL profile. Do you have any plans to integrate features of ELK with the Wikidata Toolkit [13]? How do you see reasoning engines using P31 and P279 in the future, if at all?