I have been implementing Lean for 20 years across the supply chain and ran the Lean Six Sigma organization for a major GE business.  Benefits can be quantified to show the value of using Lean to achieve critical business goals.  5S (sort, set in order, shine, standardize and sustain) does “help morale” and is intuitively a “good thing”  but can also be quantified using two metrics:

1. Lead time of a product through the shop or time to complete a job – It is fundamental in program management or basic shop floor control to know the start and end time.  If this type of data isn’t yet being recorded, it needs to be.  More output (or increased capacity) with the same people and equipment is a productivity improvement and can lead to increased revenues. Putting process in place to gather this data is the first step to making issues visible, knowing how you are performing and quantifying benefits.
2. Quality – Depending on the situation, this might be defect per unit or “job” if on a construction site, scrap, returns for poor quality, etc.  It is important to realize that as an organization moves from being reactionary to being proactive (continuous improvement mindset), it will appear that things get worse before they get better  because the problems start becoming visible.

I would make sure before you start a 5S event, that you work with leadership to find out what data is available or setup a process to capture the data in order to quantify the benefits.  And improved morale while you work is pretty awesome too!