I use it with the native trackers.
When it works, it can be fatal. For example the Aztecs can get close to the cannons or the skirmishers, but as you say it is very situational.
Improve it! Its functions could be expanded.
For example, if you upgrade ‘spies’ in the capitol or town center, it shouldn’t affect them. So they would be useful at the end of the game and in the treaty.
They could also be more effective espionage and intelligence units such as being able to identify the opponent’s metropolis destination, the technologies he is researching, what units he is creating, etc. If it is near the buildings that do these tasks.
I already made a forum about it: New abilities for 'stealth' units and rework the improvements 'spies' and 'metropolis blockade'
‘Spy’ unit could be reworked: With a ‘sniper’ type shot. Which recharges over time and costs a few coins each shot. You will kill a mersenary with a single shot, but you will pay for it.
Daimyo and Mansabdar should be vulnerable to this type of units (spies, nijas, etc).