I have been through this 10 times now and I can't get it. The closest I come is 24 but often 40-50 short. What is frustrating is I am targeting pretty much everything possible. I am holding down R2 and targeting insane amounts of bugs/bats/etc but I am simply not getting very many kills. At one point I am targeting like 30 things and I find I only have 6 kills. What the hell is going on? How is a homing target NOT killing things?
You can save in the middle check point so try that also. When you reach the end of tunnel, check the score and reload the auto save or manual save (which starts right after the cutscene)
When you multi-target, move to that region so that the homing missiles can hit them faster (shorter distance to travel). Also once you multi-target a group of enemies, target next portion of enemies not the ones you already targeted. That way you can maximize kills per shots.
Oh well I'll come back later if I actually bother finishing this game I might be just wasting my time in general. One thing I noticed is it autosaves your game half way through you can load it if you had a good first half.