factoriopedia, and other GUI elements can get "entity/icon" spam due to duplicate entities being generated in menus, which in more severe cases (with quality adding mods, for instance) can become rather....significant/hilarious/annoying

Adding the hidden_in_factoriopedia flag is easy enough and will be in the next release.
Hiding the entities in other menus is more complicated: you might need to use the icon in some mods, eg when scanning for the number of quality entities with AAI programmable vehicles, or in the upgrade planner to select the correct source entity.
Completely hiding the entity might or might not also cause some issues with blueprinting...