Decades of cognitive science establish that humans navigate environments by forming cognitive maps, defined as allocentric and topology-preserving representations of 3D space. While modern Vision-Language Models (VLMs) demonstrate emergent spatial reasoning from 2D egocentric inputs, it remains unclear whether they construct an analogous 3D internal representation. In this paper, we demonstrate that current VLMs do possess a latent topological map of 3D scenes, but it is heavily overshadowed by non-geometric visual semantics, such as color and shape. By isolating this spatial subspace through cross-scene linear feature extraction, we extract a clean spatial subspace that causally controls the model's spatial outputs. We mathematically shape this latent representation and prove its correspondence to the Laplacian eigenmaps of the scene's 3D Gaussian-kernel graph, converging to the physical 3D space in the continuous limit. Motivated by this geometric identification, we further introduce a mathematically principled latent regularization method for VLMs, based on Dirichlet energy. Applying this single-term regularizer to a minimal 500-step supervised VLM fine-tuning (SFT) on simple synthetic data yields significant improvements on real-world spatial benchmarks, outperforming standard SFT and competitive baselines by up to 12.1\% in spatial tasks involving scene topology understanding. Source code is available at https://github.com/pittisl/vlm-latent-shaping