Dear Sir and all!
You are right when you say things were not black and white. But, they were not even so simple.
For example, there are differences between codes and ciphers.
The codes are relatively simple, and used on tactical levels. For example, communications between ships in one convoy, and between escort carrier and the planes etc.
Sometimes even better radio interceptors could to break codes, especially if the participants in the communication made errors in using the codes- for example when they first send message coded, and later (because of some reasons) open- en clair.
Ciphers are different. They are much more complicated, and for any cipher it need much more time, and knowledge, to break it.
Even when a cipher has been broken, it still could be of no great use, if the broken messages don't come in real time, i.e. during the period when knowledge of enemy messages could be used against the enemy.
The British succeeded it, firstly by means of the Bombe and later in war, by the Colossus.
Immediately after midnight of the each day, the people from the BP began their job over and over again, in order to find the combination of the day- and they became faster and faster in the job!
The best decision of the British was that their codebreakers cared also about their ciphers- thieves are the best guards, if I may say so
And they kept the system until these days- of course that good ideas have to remain!
And, it is not easy to introduce completely new system of codes and ciphers, especially in war.
It is not enough to find new system(s)- new machines (in the case of the new mechanical cipher) have to be construct and manufactured, the new material (like manuals etc) have to be print- and all that have to be distributed to all units. And, after all, the personnel have to be trained in new codes and ciphers!
Finally, the new system(s) have to be introduced into service simultaneously!
It is always the weakest point- very often the cipher personnel first send the message in the old cipher, and later, after realized the mistake, in the new cipher system. perhaps looks too stupid, but it is actually too often- even once is too much! And it is the biggest mistake in codin and ciphering.
Because of that the Kriegsmarine didn't change the Enigma machines, although they doubted in possible codebreaking. They added the fourth rotor, and it was all they could to do at the time.
Of course, they didn't know that the British mechanized the codebreaking- it was the main difference between German and allied codebreaking.

But, of course, I am agreed that many questions wait for the answers!

Best regards!
Funkmeister