Given that (if I understand you right) there will be multiple photodiodes activated at once, and photodiode output is binary (only ON or OFF) then I would;
1. group them in banks of 8 photodiodes
2. use a parallel latch to "grab" each group of 8 photodiodes
3. those 8 signals are now output on the 8 output pins from the parallel latch
4. then read those 8 pins into your microcontroller in one read
It would require parallel latch ICs that have tri-state outputs, but fortunately these are common and cheap. And obviously one latch IC for every 8 photodiodes.
It should be reasonably quick as it will only take a number of microseconds to set the latch and read 8 photodiodes.