DR applies to spy ops as well. unlike normal DR, for spy ops makes it harder to succeed the ops.
the missiles you can have in your country at any one time is directly related to your country's land size.
even at max tech for SDI, its still only 90% (98.9% for demo). 1 out of 10 missiles will still get in.
There's still a random element so godly spal vs 0 spal can still fail, but it's bad luck.
More likely your target has been 'spied out' as mentioned. Between about 30 and 50 ops you start losing like 90% regardless of ratios.
The tech isnt useless though, esp if you can get it for around 1k.
Missile production for me seems to be lackluster every time I need it. fluff happens I suppose.