Because your data ranges are different.
The area underneath the curve spanning -89.5:0.001:89.5 is approximately 180/pi times larger than the area underneath the curve spanning -pi/2:0.001:pi/2.
Your answers are correct, except you are using two different ranges. Surely the comparable range in degrees is -90:0.001:90
Note also that the step size for your degrees makes that calculation much more accurate than your radians range (which is using the same step size).
[edit] Compare apples with apples...
xd = -90:0.001:90;
yd = 1./secd(xd);
xr = xd * pi / 180;
yr = 1./sec(xr);
% Use radians for x-axis in both calculations
zd = trapz(xr, yd)
zr = trapz(xr, yr)
