I don't even think you need SIP disabled to do this. System apps do require sudo for chflags to be able to edit them.
Code:
# hide
sudo chflags -h hidden "/Applications/Someapp.app"
# show
sudo chflags -h nohidden "/Applications/Someapp.app"
Toggle hidden status script (requires xcode command line tools for GetFileInfo)
Code:
for f in "$@"
do
status=$(GetFileInfo -P -av "$f")
if [[ $status = 0 ]]; then
sudo chflags -h hidden "$f"
else
sudo chflags -h nohidden "$f"
fi
done
It's actually very easy to hide them. They will only reappear after updates if the application has been modified. The process of hiding apps if very simple if you're vaguely familiar with terminal and it's no work at all to make a script that you run after an update to hide all of the system apps you want hidden.