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In the realm of healthcare analytics, sparse and irregular longitudinal health records pose significant challenges to traditional representation models, often treating missing data as mere artifacts to be imputed or discarded. This conceptual manuscript proposes a paradigm shift by framing missingness itself as an informative signal within a representation theory tailored for electronic health records (EHRs). We introduce the irregular signal encoding architecture (ISEA), a theoretical framework that integrates missingness patterns into core data representations, enhancing clinical decision support without empirical imputation. Drawing from clinical AI architectures and healthcare analytics infrastructures, ISEA comprises layered modules for signal extraction, temporal irregularity mapping, and sparsity-aware integration, fostering interoperability across EHR ecosystems. Theoretically, this approach mitigates biases in decision pipelines by leveraging missingness as a proxy for unobserved clinical dynamics, such as patient non-adherence or resource constraints. We outline governance mechanisms to monitor representation fidelity and discuss infrastructural implications for deployment in heterogeneous health systems. Formulas for decision confidence and risk propagation underscore the interpretive value of missingness, promoting robust AI governance. This theory advances EHR intelligence by reconceptualizing data voids as actionable insights, paving the way for more resilient healthcare analytics without relying on simulated experiments or performance metrics.