How to design a relational DB to capture the same entity as reported by multiple sources?
Is it poor design to have a table (i.e. Instrument) with only a single surrogate column? If this is a problem, how would it be designed differently?


If that is the only constant property of the entity then that is fine, but I would assume that there are other invariant properties such as a name ("Walmart" in your example). Even if the same "instrument" can be referred to by different names by each source and issuer (those names then belong in the relation table) do they not have a canonical name?


  Are the various *Instrument table names confusing? If so, how could it be more clear?


It depends a lot on how well you document them and/or the names and naming conventions in your target industry.

Table names should be as descriptive as possible (you can always shorten them in queries using aliases) avoiding generic words where possible. Where a generic name is needed because nothing more speciifc isn't too specific then I would suggest the simplest generic word that fits (item, object, thing) rather than instrument, but that is personal preference.

For junction tables (relation tables, or whatever you call them as there are several common names for the same concept) I recommend the name represents the row entity types in the relationship - so IssuerInstrument rather than MasterInstrument in your diagram.