Optimum locations for nitrifying bacteria:
High oxygen
Ammonia
These 2 things require good water flow to refresh the oxygen and ammonia so the organisms will be on pretty much all the surfaces that otherwise suit them, including all the filter media, and on all the surfaces in the tank. I would think they could colonize the leaves and stems. Is there some research that says they do not?
Low or no light
So they won't be on the uppermost surface of the substrate, leaves or hardscape items, unless these surfaces are shaded by plants. The substrate often is, in a planted tank. They will grow on the underside of the particles, and in the next few layers, but as soon as the water movement slows, so there is less oxygen and ammonia, the bacteria population drops. Bacterial can grow throughout the substrate if you use an under gravel filter system. I understand aquatic plants can add oxygen to the substrate, so I would suppose these bacteria could grow next to or on the roots, if there is also ammonia.
Benefits of bio media in the filter:
Very good benefit in a fish only tank. While these organisms will colonize all the media, in a fish only tank there needs to be a lot more bio filtration because there are no plants helping out. Sponges and floss can get clogged with debris, leading to lower water flow, so low oxygen. The bio media, being more open, will not clog so fast, and will still have some water movement, even if the water is following a path around the sponges.
In a well cared for filter the sponges and other mechanical media will not get so badly clogged, but this means they are getting cleaned more often. This disrupts the bacteria some. Not much, though, and they recover fast. Still, having some media that is specially designed for optimum flow specifically for the nitrifying organisms, and the maximum surface area means that there will be a very large population of these organisms in the bio media.
In a planted tank I see a lot less need for specific media just for the nitrifying bacteria. They will grow on most surfaces in the tank and filter, and there is less need for them, since the plants are part of the bio filter.
I keep a small amount of bio media in my filters (perhaps 25% of the media is specifically designed for microorganisms). I use a lot of coarse and medium sponges, and some floss as mechanical. Depending on the tank I may add peat, coral sand, or other chemical media. The bacteria may colonize the coral sand, but I doubt there is much of a bacteria population in the peat moss. The floss and peat get replaced often enough that any bacteria that get established are soon lost.