In a way it is possible.
A plugin by definition is a file that has the plugin header and it is located either at the plugins directory, or one layer "lower". If all of your custom plugins are just one file each, it will be easy to create a directory structure as you wish. Bigger plugins can technically also be done this way, but from a development POV you will probably find it harder to manage the development of each one of them and create an update flow (git for example assumes that the whole subtree of a directory belong to one project, and it will be hard to manage several subtrees on the same directory).
It should be much easier to make a one big plugin organized as modules, with a control panel that controls the modules. This should be good enough since functionality like updating and deleting is not relevant to your custom plugins.
OTOH you should probably consider just moving those plugins into your theme code. While the overhead of having code as plugin is probably zero, it is just pointless to have such a separation between parts of your own code.