I imagine that a minimap could help with that, or showing nearest neighbors at the edges of the viewport, and perhaps being able to alt-tab between applications as well as groups would help.
You can use space to have a visual organisation of things, but you don't have to navigate the space since it's virtual. You should be able to navigate suitable to your platform running the viewport.
Pinch-to-zoom, drag to move, two-finger tap to bring up list of applications to move to instantly on a tablet.
Keyboard based navigation and manipulation of the canvas if you prefer to not use a mouse on your workstation.
Click to drag and scroll-to-zoom to navigate with a mouse, when that is more appropriate, for example.
You can use space to have a visual organisation of things, but you don't have to navigate the space since it's virtual. You should be able to navigate suitable to your platform running the viewport.
Pinch-to-zoom, drag to move, two-finger tap to bring up list of applications to move to instantly on a tablet.
Keyboard based navigation and manipulation of the canvas if you prefer to not use a mouse on your workstation.
Click to drag and scroll-to-zoom to navigate with a mouse, when that is more appropriate, for example.