Okey, as this seems to be a little longer and I need support for pdepend in sonar, i have hacked a "solution":
Rename your pdepend command to pdepend_orig and create new pdepend command:
echo "Renaming files that uses traits to *.phphide"
grep --files-with-matches -re "use .*Trait" . | rename -v s/.php/.phphide/
find -name "*Trait.php" | rename -v s/.php/.phphide/
echo "Running original pdepend"
pdependorig $@
echo "Renaming files that were hidden back to *.php"
find -name "*.phphide" | rename -v s/.phphide/.php/
It hides files where you are using Traits and traits that it is excluded from pdepend. As a hack, it works.