The way i see these pacts, is that they are a promise, if you sign a co-operation pact, you are promising the civ you will be thier friend and not thier rival, if they ask you for a favour in the future by sgining this your promising your co-operation, and if you break that promise they'll hate you.
Similar with secrecy, your promising to not be the friend of one particular civ, and if you go backl on your word, you'll annoy your new found friend.
basically you should be signing co-operation pacts only with civs you view as valuable friends, and signing secrecy pacts against only civs you consider to be cun..........ningly annoying civs.