Junco does indeed mean junk. It's jonque in French and it meant old bits and scraps of rope and stuff used for ships' caulking long before it meant heroin (early 20th century.)
Junco is also a Portuguese sailor word for caulking material but it's more directly related to the “reeds” the French word ultimately traces back to. Same as the straw to fix a hole in a wooden bucket.
All three words, and too many cognates to list, also describe the same Eastern sailing vessel.
Junkanoo is Protestant. They'd be out on the levee in this genre. The majority Catholics get crazy at Carnival-Easter-Mardi Gras in town. As in another thread, one church believes The Saints will come marching in one day, the other not so much.
The character of John Canoe can be anything from a living Jack Pudding to a puppet (bwa-bwa,) depends on the place and the century. Like griot, the etymology may have common roots but the traditions are a mixed-up mess.