Depends on the type of tank and light setup...
If your doing a reef and have heavy duty MH lighting you may not want bright light 'glowing" out the back of you canopy, if so then just cut out for the filter...
If you DIDN'T have the HOB filter you could push the tank/canopy against the back wall and it wouldn't matter..
For FO tank with normal output lights the glow out the back may not be annoying...
Mostly personal preference...