I've found of "The Shapeless" to be a fitting name because of a couple of things. It's one of the traits of the "Shadow People" (also known as a shadow figure, shadow being or black mass),  the perception of a patch of shadow as a living, humanoid figure, particularly as interpreted by believers in the paranormal or supernatural as the presence of a spirit or other entity. I'd say this would be fitting to the aspect and nature of this faction. Not only "alien" to humans but also other sentient creatures, machine and organic. Those sleeping, with heightened emotion and -metanphetamine addicts- see "shadow figures", which may have spawned many folklore perceptions of the supernatural in our history.
It could also refer to their society/culture in an array of ways.

"You don't see shadow dogs or shadow birds or shadow cars. You see shadow people. Standing in doorways, walking behind you, coming at you on the sidewalk." - Methology Pt 1

- Let's wonder some lore
The Shapeless are mighty in their infiltration and camouflage ability. While it's partly thanks to their remorseless philosophy, it's mostly because of their shapes, or rather, lack thereof. Other beings, biological, mechanical or other, find them to be such an incognita of a species that they will assume their presence as a manifestation of Pareidolia (perceiving a vague stimulous as a shape). Even between each other and themselves, the Shapeless species and civilization may be referred by the same name, still as wiling to make their place in the galaxy as any other.