Never mind the systems issues, having the engines buried in the wing root creates significant design, performance and maintenance challenges. Going from a turbojet to a turbofan and increasing the space required just exacerbated those issues. During the upgrade program it was discovered that no two airframes were alike, despite BAE's claim of Nimrod "being the best understood airframe in service". The design was flawed from the start, and the Ostrich mentality that ignored the obvious was responsible for the cost and delay still impacting the maritime capability today.
This is pretty much spot except as mentioned above this was completely common knowledge in the 70 late alone later. Many of the airframe issues came up during the ill rated AEW debacle (funny how often that fails to get a mention) and you can even roll back the lack of space issues to the 1960's comet v 707.
Military folk with decades of maritime experience, on the ground and in the air, were venting their frustrations about all of this in 1990's and as I've mentioned before, I, like many others, was ordered to "get with the programme" by the then staish.
I was at BAE on a course in May 1998 when a crew chief uncovered a previously unknown issue with the bomb doors. It was a headslap doh moment. Pretty funny really, except for the 3 billion plus tax payers money down the swanney and 10 years (maybe more?) with no kipper fleet.
Still well-played BAE Marketing Team...that was some stunt you pulled off there.
edit cross posting Haraka...answer yes, and they were all know and out in the open from the get-go.