Per my understanding:
Raising the agreements on Equite and Scouts will increase their spying ability in addition to normal offense and defense. Increasing spying ability makes your scouting units more powerful when spying on a city (you lose less and have higher chance to succeed) and when defending your city against spies from an enemy (enemy loses more and have lower chance to succeed). Go to the stables building, take your mouse and hover over the spying information for the Equite/Scout and you will see what bonus you are getting there.
Like with any agreement upgrades, the bonus is small across a few agreement levels only. If you scouted with 100 level 25 Scouts, and thereafter with 100 level 30 Scouts your spying ability was only approximately 7% stronger on the second attempt. In comparison, it is as if you sent 107 level 25 Scouts on the second attempt. So, it is not surprising that you aren't really noticing something with the 5 agreement levels, because it is a small bonus.
The agreements on Scouts/Equites are still worth getting because they will save you a lot of scouts in the long term. If you are sitting with +/- 100 Scouts only, the best way to increase your scouting ability is just to build more scouting units. You can see, for example, if you have 1000 + scouts, then increasing agreements start to make a bigger difference. Consider the screenshot above from Drag-Theseus: If that player had scouting units agreements on level 0 versus on level 30, and if the scouting defense was only a little bit stronger, the difference would be many days (maybe even weeks) of scouting units saved in terms of building time, in a single scouting mission. Also, every player needs a good number of scouting units available. Since higher agreement levels mean you lose less scouts, this means you have to replace fewer scouts, which means more time for you to build cavalry offense/defense units.
