That's a broken system regardless of whether anything is bundled or not. If module X has a dependency on module Y, this is an implementation detail of module X

That's a broken system regardless of whether anything is bundled or not. If module X has a dependency on module Y, this is an implementation detail of module X and should be completely encapsulated in module X. If for some reason the system needs every copy of module Y to be the same singleton object in memory, then you need to create that instance centrally and pass it around to whoever needs it, not just rely on the Node's require cache mechanism to hopefully return the same copy for two separate require calls in different places. That may be how the require cache works, but that's an implementation detail of Node and not the right way to ensure something is a singleton.