These ideas make sense, so should we assume that removing the molded black plastic pieces and replacing them with straight hose tubing would not harm anything except for producing more noise?

Whatever is done when people install aftermarket intakes would apply here. If there's a vac line to be plumbed somewhere, you need to do that; if plugged, then do that.

Breather tubes with filters.

Not everyone wants their car to be louder...

I was wrong...
 

They also serve as PCV's -- you would need breather filters as someone else noted.