I'm answering my own question only because I happened to find a 4th solution--a needle in the haystack. I did some ldd testing on /usr/bin/nx*, which strangely didn't return the information matching my dynamic libraries that I was expecting. grep on the same files just happened to find this block in /usr/bin/nxloadconfig:
#########################################################################
# INTERNAL STUFF
# DO NOT TOUCH unless you REALLY know what you are doing
#########################################################################
NX_VERSION=3.2.0-74-SVN
NX_LICENSE="OS (GPL, using backend: %BACKEND%)"
# Where can different nx components be found
NX_DIR=/usr
PATH_BIN=$NX_DIR/bin # if you change that, be sure to also change the public keys
PATH_LIB=$NX_DIR/lib
NX_ETC_DIR=/etc/nxserver
NX_SESS_DIR=/var/lib/nxserver/db
NX_HOME_DIR=/var/lib/nxserver/home
# Advanced users ONLY
AGENT_LIBRARY_PATH="" #Calculated
PROXY_LIBRARY_PATH="" #Calculated
APPLICATION_LIBRARY_PATH="" #Calculated
APPLICATION_LIBRARY_PRELOAD="" #Calculated
# the name of the authorized keys file for ssh
SSH_AUTHORIZED_KEYS="authorized_keys2"
I manually edited PATH_LIB=$NX_DIR/lib to PATH_LIB=$NX_DIR/lib/NX/lib and now the only missing files are actually missing (libXcomp.so.2)