Turns out those classes and their methods are referenced in functoids.
If you open a .BTM file (mapping) you will see how data can be manipulated by these between the source and target schema.
By "Configuring Functoid Script" you can select either Inline C#, JScript.NET and others to perform certain operations on the flow of data between the source and target schema. One of these options is "External Assembly" where you'll be able to select a method from a class that you have referenced in your project.
By "Configuring Functoid Inputs", you'll be able to configure the parameters to be sent to the "External Assembly"'s referenced method.
By searching in "Entire Solution" for the method's name, you eventually find it mentionned in the XML content of the .BTM file. Open the BTM file (by just double clikcing on it in your solution) from there, look for all these "S" symbols in the grid, that's where it'll likely happen.