Given that clojure "embraces the platform", it'd probably be pretty hard to have clojure.net _without_ ikvm in there somewhere. Performance could be increased by porting the code generator and core classes to .net, but users expect to use arbitrary java libraries, so that capability has to be there.
(Seems like that strategy could also be applicable to a native port, using an embedded jvm to handle whatever has not been ported from java land)
and FWIW (i have little .net knowledge)
ubuntu:~% ikvm -jar clojure.jar
Clojure
user=> (. cli.System.IO.File OpenText "/dev/null")
#<StreamReader System.IO.StreamReader>
(startup takes about 6x times as long with ikvm than java -client. compiling with ikvmc creates a clojure.exe which instead takes 9x to start. clojure-1240 non-slim, java 1.6.0_07, ikvm 0.34.0.4, mono 1.9.1)