You said "map" but are talking about "tree". There are other ways maps can compose, e.g. graph, which do not lead to deep nesting and transformations.
In essence yes, the maps I see being bandied about in clj tend to have tree structures.
Haven't seen much/any use of graphs in clj code. Deep nesting has become almost idiomatic at this point from my POV.
Could you provide example/pointer to clj code using a graph in lieu or in addition to a map?