The sage business guru Willie Sutton might answer the question "Why must we work so hard at digging to finding the causes to our problems?" by observing "Because that's where the roots are." Digging to find root causes is hard work. They're are rarely obvious and there's never just one. Occasionally, you might get lucky and trip over an obvious root cause (obvious once you've tripped over it.) Most often, it'll require some unknown amount of exploration and experimentation.
Even so, I've watch as people work very hard to avoid the hard work needed to find root causes or fail to acknowledge them even when they are wrapped around their ankles. It's an odd form of bikeshedding whereby the seemingly obvious major issues are ignored in favor of issues that are much easier to identify, explain, or understand.
One thing is certain, you'll know you've found a root cause when one of two things happen: You implement a change meant to correct the issue and a whole lot of other things get fixed as a result or there is noisy and aggressive resistance to change.
Poor morale, for example, is often a presenting symptom mistaken for a root cause. The inexperienced (or lazy) will throw fixes at poor morale like money, happy hours, or other trinkets. These work in the very short term and have their place in a manager's toolbox, but eventually more money becomes the new low pay and more alcohol has it's own very steep downside.
Morale is best understood as a signal for measuring the health of the underlying system. Poor morale is a signal that a whole lot of things are going wrong and that they've been going wrong for an extended period of time. By leveraging a system dynamics approach, it's relatively easy to make some educated guesses about where the root causes may be. That's the easy part.
The hard work lies with figuring out what interventions to implement and determining how to measure whether or not the changes are having the desired effect. A positive shift in morale would certainly be one of the indicators. But since it is a lagging indicator on the scale of months, it would be important to include several other measures that are more closely associated with the selected interventions.
There are other systemic symptoms that are relatively easy to identify and track. Workforce turnover, rework, and delays in delivery of high dependency work products are just a couple of examples. Each of these would suggest a different approach needed to resolve the underlying issues and restore balance to the system dynamics behind a team or organization's performance.