Have you looked at the VAAs, with cumulative upstream area, arbolate sum, and more arcane things like LevelPathID? These VAA attributes are very useful sometimes when manipulating NHDPlus.
Also, the NHD now includes a scale attribute that can be used to select out tiny features you don't want when displaying at smaller scales. This is a new update to the NHD data model, and USGS would love some feedback if you find it useful (or not).
Not really a spatial analyst question so I am tagging Arc Hydro as folks there may have more to add.