It will simply be an on/off system. So do you recommend using the ATMega?
Only if you haven't bought any hardware, yet - if you already have the Arduino 2009, then going with a shift register or centipede shield would probably be a better idea - unless you think your software will end up being larger than what your Arduino can support.
Where is the centipede sheilf available to buy?
I see that someone has already answered this...
With this type of project, will it simply be attaching the sensors directly to the board?
Sorta - you might need a resistor or such for pull-down reasons, but more or less, yes. You might also need to build a driver circuit for the lasers to turn them on and off (unless it will be a manual thing with a switch), but that is fairly simple to do.
One thing you will have to look for is to match your phototransistors to the laser's wavelength; some phototransistors have a wide bandwidth they can sense (visible light to IR), some are only sensitive in a narrower band (typically the IR region). So try to find spec sheets on the phototransistors before you decide and buy...