You can use logical indexing to replace for loops. It's hard to fully understand what is happening in the "comb_array" line since you are referring to the variable on the left side of the equation with 3 dimensions but on the right side only with 2 dimensions. However, the optimized code should look something along the lines of:
row_delay = 1:num_row_dealays;
hole_delay = 1: num_hole_delays;
row_num = 1:num_rows;
hole_num = 1:num_holes;
%
x = design_array(row_num,hole_num); % Array has either 1 or 0
ftime = hole_delays(hole_delay(x)) .* hole_num(x) + row_delays(row_delay(x)) .* (row_num(x)-1); % hole_delays predefined
%
comb_array(row_delay(x),hole_delay(x),ftime) = comb_array(row_delay(x),hole_delay(x)) + 1;