The solution is to manually set the LANG environment variable before executing Java on the init script:

LANG=en_US.UTF-8
export LANG

Here is my full init script for reference:

description "start/stop Ubooquity"
author "lapause"
start on started httpd-user
stop on runlevel [06]
setuid http
script
   JAVA_DIR=/volume1/@optware/opt/ubooquity/env/ejre1.7.0_75/bin
   WORK_DIR=/volume1/@optware/opt/ubooquity/var
   PORT=2202
   # $MEM=-Xmx512m
   LANG=en_US.UTF-8
   export LANG
   exec $JAVA_DIR/java -Dfile.encoding=UTF-8 $MEM -jar $WORK_DIR/Ubooquity-1.8.2.jar -port $PORT -workdir $WORK_DIR -webadmin
end script

All my folders and filenames with accentuated characters are now fully recognized when Ubooquity is started from init script.