I'm curious about where all the current ROMs available came from
(mainly because unlike discs, cartridges are not typically supported
by standard hardware).
There are basically two kinds of ROMs -- images of commercial titles obtained through questionable legal means using cartridge dumping hardware, and images of homebrew titles that are written directly from your PCs memory to disk via the homebrew SDKs that are floating around. Most of the ROMs you are probably thinking of are the former kind. Cartridge dumpers are essentially hardware, sometimes custom-built, that copy the read-only memory chips on a cartridge to disk in some format.
By any chance is there still a serious reason why the tools are still
There is no business advantage to Nintendo to make the tools available. They would turn no profit from it. Plus, especially for older consoles, many of the older official SDKs talk with proprietary hardware (dev kits) that may not even be in production any longer, so there's very little you could likely do with the toolchain from Nintendo.
Homebrew console SDKs produce ROMs because emulators already exist. It's unlikely that most official SDKs produced ROM images that could be consumed in exactly the same fashion.