If there are one or more directory whose last part is the same, the second one is ignored.
:~/svn$ sloccount DBS/trunk/ CRM/trunk/
Creating filelist for trunk
WARNING! Directory trunk pre-existed when adding CRM/trunk/
SLOC Directory SLOC-by-Language (Sorted)
56608 trunk java=54342,xml=1941,sh=170,python=155
Basically this should be possible: particularly in the case of a complex repository, lots of directories end with /trunk :)