Of the many possibilities for troubleshooting a hydraulic system, pressure gauges in a few key areas are helpful. One important place would be pressure checks at the thruster inlet, any motor bypass lines and outlet.
A hydraulic shop should be able to supply a guy with the right gauges and know where to install quick connect fittings for the gauges to get plugged in for system checks. This then allows you to isolate problem area which could be the main valve block, check valves, manual valves, thruster motor or hydraulic pump.
Possibly the original install or design is at fault and problems have existed since day one. Wesmar should be able to proved an ideal install schematic to compare to actual.
Yes, everybody claims to love hydraulic thrusters. I am not one on smaller vessels. Electric thrusters are not the menace some say and even Nordhavn equips the vast majority of their sub 60 footers with electric. I debated this issue a few years ago with my vessel and ended up with electric which can run uninterrupted for in excess of one minute, that was the extent of my test. I also went through this with Nordhavn when specing out a new build. If per chance you need some expensive repair parts, it would be nice to have the cost of a 8kw or so electric thruster in your back pocket. The hole is already there.
Last but not least get a really bright flashlight and look at all the system's valve bodies and fittings for hairline cracks and fluid loss.