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).
 Compare apples with apples...
xd = -90:0.001:90;
yd = 1./secd(xd);
xr = xd * pi / 180;
yr = 1./sec(xr);
zd = trapz(xr, yd)
zr = trapz(xr, yr)