Well, if you need to run flashed carts, then yes, they are custom hardware. Downloadable titles can be debugged and run on normal 2DS/3DS hardware with the IS-SNAKE according to the site, which still costs over $2K. The dev units themselves are fairly reasonably priced considering they'll have additional memory for debug builds, etc, and cost a reasonable amount - the problem is the flash card writer and debugger hardware that is needed to actually use them.
Actually, I was wrong, the IS-SNAKE is a complete "New 3DS" dev kit. These devices are resource constrained, so you need more memory, CPU, etc to be able to properly debug anything on these devices.
