But, flood zones aren't always associated with rivers. Some places are just really low and have poor soil drainage and/or high water table and during a large storm event will flood. The FIRM maps show flood zones out to areas that flood for a 500 year storm and those areas must be accounted for if developed within.
I agree.
Any area that has historically flooded should be documented already, but that does not mean new ones cannot be created by construction, highway projects, and alterations to surface permeability.
Topographic contour data should be available in GIS format or hard copy as well, which permit the delineation of drainages, whether highly organized, estuaries, or inland basins.
While the Corps may not have everything, I'd wager the 'intermittent wetlands' are documented either there, or at EPA who has had dreams of (and actual accounts of) suing people for filling low spots in their yard after deeming that low spot to be an 'intermittent wetland'. Soils data should be able to confirm or deny wetland status in the past.
The 100, 200, and 500 year flood plains are an actuarial feature, based on topographic information and anticipated flood volumes.
Anything which impedes the flow of water through the watershed at a specific volume must be taken into account, whether levees, bridges, culverts, or the like because it can create impoundments at that flow rate and above which would not exist at normal flows, that complicates the problem, because the duration of high flow states will affect the amount of water caught in that and how far it spreads over any given topography.
Overtopping or destruction of those impounding features can relieve the impoundment beyond that stage, but there will still be additional areas inundated as the water rises.
It is complex enough that you'd want competent hydrologists working on the problem, just from the viewpoint of the impact of additional structures or impermeable surfaces changing the flow characteristics of the watershed, be that a river or a natural (or even artificial) impoundment.
Those personnel will cost money, and it is more likely that competent personnel could batter be retained at the State Level and have the resources available to adequately assess the impact of proposed construction, than at the local level, unless that locale is a major urban area. .