Oracle Apps - Not quite as sure about it, but I believe its origins
predate the use of referential integrity in the database.
I worked on Oracle (UK) Accounting v3 during mid-late 80s, some ideas from which (code combinations for example) were 'borrowed' for what became Oracle Financials. AIRC that was around 1987-8. HR development started a little later, and being UK based was a lot more CASE (Oracle Designer) inclined (they shared the same building). Manufacturing originated in the US consulting organisation, and again they were somewhat more methodological than the original Apps team in Redwood. In both cases I think initial development still pre-dated the implementation of effective foreign keys in Oracle 7. For Financials, even the option of FKs in the dictionary was not yet on the menu.
The (defensible) strategy to 'disintegrate' the applications (eg having separate GL, AP, AR modules in Financials) made it easier to get early releases out of the door - but at the cost of hiding relationships. And of course the whole Application Foundation ethos of configurable code combinations and flexfields means that many relationships are impossible to implement as Oracle serverside constraints out of the box.
Since then, I guess the normal product development priorities have reigned: functionality/saleability first, customer bug fixes second, and engineering/non-functional improvements last. Performance fixing priority goes up and down the scale according to the level of pain being felt by critical customers (Cary Millsap will remember performance testing of release 9, for example).
Just try to explain to a VP of Applications that you want to spend (managers prefer 'invest') tens of man-years documenting and 'improving' internals. It's like painting the Golden Gate bridge - once you start, you never stop. That budget has to come from somewhere - and the other priorities always seem more attractive. So there is a tendency to maximise entropy (btw that's one of the main reasons why startups can beat gorillas).
All the large ERPs seem to suffer the same problems - it's not just Oracle. But as one poster said - the more gotchas there are in the Apps, the more work for us... in the short term at least.