What is a stealth chain in Shogun Total War 2?

Solution 1:

@iG_42 is correct, I mixed the two building chains up. Please unaccept this answer so I can delete it.

Solution 2:

The Stealth Chain refers to the Sake Den from which you initially recruit ninja and it's upgrades.

As your quote states you naturally need one den to have a single ninja and you can recruit another ninja for each additional den you construct up to a maximum of five ninja though there is no restriction on the number of stealth chain buildings you can and ninja can be recruited from any stealth chain building.

If you lose or demolition stealth chain buildings so that you have fewer than the number of ninja you are currently fielding they will remain on the map but cannot be replaced if lost.

The buildings mentioned in Dulkan's answer are special buildings only available in certain provinces that increases initial rank of newly recruited ninja agents and kisho ninja or extra income with smaller bonuses to units and agents.