When I look at miniatures of kings during the middle ages, I see that most of them are depicted holding a building in one hand. Is there any symbolism/significance behind this?
I have an earlier answer about this, if you're interested!
The birdhouse of the soul in medieval art can have a few meanings--Google reverse image search shows that the two examples you picked illustrate two of the main ones, which is pretty awesome.
Survey says the first painting (in the earlier thread) is a fresco from a Serbian Orthodox monastery that depicts the apostle Peter. He's carrying a church building on his shoulders to symbolize "on this rock I will build my Church," most likely. (From the same fresco series, Paul is not carrying the Church.)
The second example is a depiction of the patron--the person who "sponsors" a work of art (pays the artist). From the Cappela degla Scrovegni, it depicts patron Scrovegni "giving" his church building to God (that is, paying for it).
So I guess in general, I would say that the little buildings represent either the Church or a specific church and express a relationship between the person involved and the C/church.