This is one of those odd things that seems to effect different guns and tvs in different ways.
My spare tv has a 1” dead zone along the bottom.
My normal TV is a little dead on the left edge with the same guns!
Other than turning up brightness and contrast not much you can do.
Oh and make sure the screen and lenses are clean 
Thank you for your reply.
Sounds like it could be a bit of everything then! When I get a chance I'll try it with other CRTs via family and friends as well, only have the 1 at home at the moment.
I'll try cleaning in addition to increasing the in-game brightness. I'll also look into PS2 hacks to see if there is a way to decrease the screen size so it fits the game screen into the detectable area of the TV (although this might confuse the light gun?).
Thankfully it's not a BIG DEAL. While observing the enemy placements it almost feels as if the developers intentionally knew of this potential problem and let it inform their enemy placement design.
I'm actually quite happy with the AimTrak on my 50 inch LCD TV.
My main motivation with this CRT lightgun experimentation was I wanted to feel what top sliding recoil and auto recoil feel like. While top sliding is nice, it isn't a deal breaker (very noisy!!!), but I'd love to mod my AimTrak (or mod AimTrak internals into something else) to have the auto recoil functionality. It makes such a difference when using machine guns in TC2, TC3 and of course CZ. But I'm not brave enough to try modding...yet!
There's also the auto-fire feature which turns all guns into machine guns, which feels like cheating, but is so fun! Auto-Reload is another as well, but it didn't work properly the time I tried it (I think I need to unplug the Reload Pedal for that to work properly).